Fisheries Management Objectives Research Articles

An evaluation of the relative size, body condition, and survival of triploid Walleye in the wild

AbstractObjectiveNatural dispersal or unauthorized introductions of nonnative predatory sport fish can undermine native species conservation and other fisheries management objectives. The use of reproductively sterile triploid fish may provide a lower risk stocking option (i.e., genetic and reproductive containment) for diversifying angling opportunities while possibly reducing angler motivation to illegally transplant fish. Management interest in triploid Walleye Sander vitreus is growing, and these fish are currently stocked by several fisheries agencies. However, little is known about the poststocking growth, body condition, and survival of triploid Walleye—information that is important for calibrating expectations and guiding policy regarding their use.MethodsWe compared the age‐specific size, body condition, and survival of subadult (i.e., ages 0–3) triploid Walleye to those of normal diploid conspecifics in two eastern Colorado reservoirs. Paired stockings of triploid and diploid Walleye occurred over 3 years. Both fry and fingerlings were stocked each year.ResultTriploids were generally smaller in length (6.6% smaller on average) and weight (20.6% smaller) compared to diploids across all age‐classes. Despite being smaller, triploids had similar body condition relative to diploids. On average, the survival of triploids from spring stocking to their first fall was 6.3× lower than that of diploids, but no differences in survival were observed beyond this early life stage. This pattern was consistent across cohorts and reservoirs.ConclusionThe present work provides a foundation for future studies that are designed to clarify patterns of survival from spring to the first fall by accounting for size at stocking and natural‐origin fish and studies that are planned to assess the poststocking performance of triploid Walleye independent of diploids.

Modelling perspective on the climate footprint in south east Australian marine waters and its fisheries

Abstract South eastern Australia is a global warming hotspot, and is also home to ~70% of Australia’s population and one of Australia’s largest fisheries—the South East Scalefish and Shark Fishery. This fishery spans shelf to deep waters, subtropical to temperate waters, employs many gears, and interacts with over 100 species. Despite following best practice fisheries management principles, including taking an ecosystem perspective to overall fisheries interactions, management interventions have failed to arrest or recover the decline of some focal species. Using an Atlantis ecosystem model developed for the fishery over the past 20 years, this paper presents simulations that suggest climate change may be a major contributor to the trajectories seen for a number of species—such as jackass morwong (Nemadactylus macropterus), blue warehou (Seriolella brama), and gemfish (Rexea solandri). This kind of climate influence poses many challenges for fisheries management into the future, raising questions about what to do when climate change undermines or overrides fisheries management actions and objectives.

A comprehensive functional form of the optimal harvest control rule for multiple fishery management objectives

For many of the world's fisheries, harvest control rules (HCRs) are the main tools for supporting decision-making. We previously clarified the optimal shape of the HCR to achieve multiple fisheries management objectives (maximising average catch, reducing variation in yields, and avoiding stock collapse) and ensure robustness to estimation errors in biomass by numerically estimating the optimal values of the 21 biological reference points (BRPs) comprised in the HCR. However, for actual management, a simple but comprehensive functional form to emulate the optimal HCR is desirable, as numerical HCR optimisation with many BRPs is time-consuming. Here, we introduced three objective utility functions ( U1– U3) representing HCR performance for composite management objectives: mean–variance utility functions, where the performance indicator for variation in yields is the standard deviation ( U1) or the annual average variance ( U2) of yields, and the constant relative risk aversion utility function ( U3). We derived two equations to emulate the optimal HCRs with three adjusting parameters corresponding to the management objectives and different magnitudes of estimation errors. These equations will help stakeholders discuss desired management strategies by showing expected catch and risk by adjusting the parameter values.

Valuation of fisheries management status based on ecosystem approach (EA) in East Simeulue, Aceh

Fishery management is an activity that must be carried out to achieve sustainable fisheries. Fisheries management using the Ecosystem Approach to Fisheries Management (EAFM) approach is the sustainable use of fishery resources and protection of fish stocks in nature. One of the objectives of fisheries management in social and economic aspects is how fisheries can ensure the socio-economic welfare of the fishing community. Using fishing gear that is not environmentally friendly is one of the triggers for social conflict between fishermen and the uncertain selling price when the peak season of fish impacted the fishermen's economy. Therefore, the purpose of this research is to examine the socio-economic domain indicators from the aspect of EAFM-based coastal and marine resource ecosystem management. This research was conducted from January to February 2021, located in Simeulue District, Sub-District East Simeulue. The data collection method used in the study was interviews and field surveys. The determination of respondents is done by using a gradual sampling technique or stratified random sampling. Data analysis uses an ordinal-based Likert score of 1,2,3 for each indicator, namely the economic domain, fishery household income (RTP), savings ratio, asset ownership, and the social domain, namely stakeholder participation fisheries conflict and the use of local knowledge in fish resource management. Management status in East Simeulue District assessed the aggregate value of the economic domain in the medium category with a score of 48.3. Fishermen still earn less than the minimum wage, while in the social domain, it is in the excellent category with a score of 100 because fishermen, institutions, and related agencies work with each other. Keywords:EAFMEcosystem approachFishery management

Managing biological, economic and social trade-offs in the Australian Southern and Eastern Scalefish and Shark Fishery

Context Maximum sustainable yield and maximum economic yield are often advocated as desirable biological and economic objectives for fisheries management, and the analysis of trade-offs associated is often absent from scientific advice. Aims This work aims to demonstrate an operational approach for comparing trade-offs of not only biological, and economic objectives, but also social objectives, in this case for maintaining affordable fish prices for the Australian public. Methods We use a simulation model of the multi-species, the Australian Southern and Eastern Scalefish and Shark Fishery, characterised by technical and economic interactions among harvested stocks, and apply an eco-viability approach to identify catch limits on two key species of the fishery (tiger flathead and pink ling). Key results Several trade-offs are highlighted related to the distribution of benefits among vessel owners, fishing crews and consumers. Maximising the economic returns to vessel owners, which is the current management objective of the fishery, correspondingly reduces social benefits of providing employment as fishing crews and raises consumer prices. Conclusions Maximising fishery profits as a management objective comes at a social cost for crew members and fish consumers. Implications Analysing trade-offs with an eco-viability approach helps inform decisions regarding fisheries management, fully accounting for the different dimensions of biological, economic and social sustainability.

New records of Spotted Bass, Micropterus punctulatus, within the Mississippi River Basin, Illinois.

Spotted Bass Micropterus punctulatus, like many sport fishes, have experienced range expansion through intentional introductions (i.e., legal stocking and illegal transfers) and migration across the United States. In Illinois, USA, native populations of Spotted Bass occur along the eastern and southern border of the state. We report new records of Spotted Bass in their non-native range of the Illinois Waterway and the Illinois portion of the Upper Mississippi River in addition to collections in their native range in the Illinois sections of the Ohio and Wabash rivers to better understand their current distribution. Continuous, collaborative efforts to track the distribution and expansion of non-native fishes are important for maintaining and establishing native and non-native fisheries management objectives and education, as non-native fishes can influence native species population distribution and dynamics.

Risk equivalence in data‐limited and data‐rich fisheries management: An example based on the ICES advice framework

AbstractFisheries management needs to ensure that resources are exploited sustainably, and the risk of depletion is at an acceptable level. However, often uncertainty about resource dynamics exists, and data availability may differ substantially between fish stocks. This situation can be addressed through tiered systems, where tiers represent different data limitations, and tier‐specific stock assessment methods are defined, aiming for risk equivalence across tiers. As case studies, we selected stocks of European plaice, Atlantic cod and Atlantic herring, where advice is provided by the International Council for the Exploration of the Sea (ICES). We conducted a closed‐loop simulation to compare risk equivalence between the data‐rich ICES MSY rule, based on a quantitative stock assessment, and the revised data‐limited empirical management procedures of the ICES advice framework. The simulations indicated that the data‐limited approaches were precautionary and did not lead to a higher risk of depletion than the data‐rich approach. Although the catch based on generic data‐limited approaches was lower, stock‐specific optimisation improved management performance with catch levels comparable with the data‐rich approach. Furthermore, the simulation indicated the ICES MSY rule can fail to meet management objectives due to increased depletion risk when management reference points are set suboptimally. We conclude that the recent revisions of the ICES system explicitly account for risk equivalence for data‐limited fisheries management and are a major step forward. Finally, we advocate further consideration of simple empirical management procedures irrespective of data limitations due to their ability to meet fisheries management objectives with greater simplicity.

Factors Influencing Early Growth of Juvenile Tiger Trout Stocked into Subalpine Lakes as Biocontrol and to Enhance Recreational Angling

Tiger trout (Salmo trutta × Salvelinus fontinalis) are sterile hybrids often stocked as a biocontrol agent for undesirable fishes and to enhance recreational angling. Yet, how different ecological processes affect their post-stocking performance remain poorly understood. Rapid growth early in life can foster rapid transitions to piscivory, and improve survival. Identifying factors that benefit early growth can help managers optimize tiger trout stocking for meeting multiple fisheries management objectives. Here, we characterized the trophic ecology and growth of tiger trout stocked at varying densities into seven lentic subalpine systems in Colorado, USA. Study systems supported different species of undesirable fish (e.g., minnows or suckers). We used stable isotopes of carbon and nitrogen to quantify trophic relationships among tiger trout and other fishes in each system. We then evaluated several system-specific attributes as predictors for the size of tiger trout at age-1 using a Random Forest model. Stable isotopes demonstrated the potential for resource competition among tiger trout and other fishes, but potential varied by system. Indices of resource competition ranked highest in the Random Forest model, but the stocking density of tiger trout was most important, suggesting that intraspecific competition outweighed interspecific competition in driving early growth. These processes were mediated by system productivity. Thus, stocking density in combination with the realized carrying capacities of systems should be considered when making management decisions for tiger trout.

Evaluation of the economic crisis on the conservation of the ichthyofauna in Marine Protected Areas

The use of marine protected areas can be an effective way to simultaneously achieve both conservation and fisheries management objectives. The creation of marine protected areas, in addition to many benefits, also entails several costs, including the need for financing to maintain adequate surveillance and conservation. The recent economic crisis significantly lowered budgets for the maintenance of Spanish Marine Protected Areas, that may have had serious consequences for the marine resources sustainability. In this study we evaluated the indirect impact of the 2008 economic crisis on the conservation of fish stocks in Marine Protected Areas. We compared the number of species, abundance and biomass levels of the ichthyofauna, and abundance and biomass of selected species in two marine reserves (Cabo de San Antonio and Tabarca Island) with control areas, two years before (2008 and 2010) and two years after (2014 and 2015) the budget cut. Results in San Antonio revealed a decrease in total abundance, total biomass and number of species after the crisis, which translates into a decrease in the reserve effect. While in Tabarca no reduction has been observed in these variables, so the reserve effect was maintained after the crisis. We have found that of the 18 species analyzed, in San Antonio the abundance and biomass of 8 and 6 species respectively have decreased after the crisis, while in Tabarca the abundance and biomass of 6 and 8 species respectively have decreased after the crisis. Therefore, surveillance in marine reserves is necessary for the conservation of the species.

Multi‐species hotspots detection using self‐organizing maps: Simulation and application to purse seine tuna fisheries management

Abstract To fulfil fisheries management objectives that often include implementing the precautionary and ecosystem‐based approaches, multispecies fisheries data need to be analysed. Amongst the different methods dealing with these multidimensional data, self‐organizing maps (SOMs) remain rarely used, although they are highly flexible in data input and offer visualization possibilities particularly suited to summarize complex datasets. Here, we propose to combine SOMs with a clustering approach to break down data complexity and produce simple geographic maps showing catch hotspots, which can indicate sensitive zones in terms of fishery management. To promote this approach, we tested it first on simulated datasets and then on the open‐access ICCAT commercial catch database of the tropical tuna fisheries of the Atlantic Ocean. We aimed to detect drifting fish aggregating devices (dFADs) catch hotspots of juveniles of two tuna species, bigeye and yellowfin tunas and of the silky shark, a commonly bycaught vulnerable shark species, in tropical tuna purse seine fisheries. Simulations on datasets increasing in complexity (in number, geographic and duration extent of the hotspots and number of species in the analysis) informed us about the method's sensitivity and limits. Our findings showed that, in the context of multi‐specific fisheries, the detection of the hotspot is dependent on a certain level of catch within the hotspot and that adding species to the analysis tended to mask small and short‐duration hotspots. Applied to tropical tuna fisheries' data, the method confirmed the empirical knowledge on which first time‐area closures were based and provided scientifical support. All in all, the visual support provided by the method, its interpretability and its potential transferability to other fisheries' systems constitute its main strengths and imply a possible implementation in management decisions; specifically, as a tool to reach agreement between stakeholders in the definition of regulated areas for protecting juveniles of tunas and vulnerable associated species to dFAD practices.

Untangling social-ecological interactions: A methods portfolio approach to tackling contemporary sustainability challenges in fisheries.

Meeting the objectives of sustainable fisheries management requires attention to the complex interactions between humans, institutions and ecosystems that give rise to fishery outcomes. Traditional approaches to studying fisheries often do not fully capture, nor focus on these complex interactions between people and ecosystems. Despite advances in the scope and scale of interactions encompassed by more holistic methods, for example ecosystem‐based fisheries management approaches, no single method can adequately capture the complexity of human–nature interactions. Approaches that combine quantitative and qualitative analytical approaches are necessary to generate a deeper understanding of these interactions and illuminate pathways to address fisheries sustainability challenges. However, combining methods is inherently challenging and requires understanding multiple methods from different, often disciplinarily distinct origins, demanding reflexivity of the researchers involved. Social–ecological systems’ research has a history of utilising combinations of methods across the social and ecological realms to account for spatial and temporal dynamics, uncertainty and feedbacks that are key components of fisheries. We describe several categories of analytical methods (statistical modelling, network analysis, dynamic modelling, qualitative analysis and controlled behavioural experiments) and highlight their applications in fisheries research, strengths and limitations, data needs and overall objectives. We then discuss important considerations of a methods portfolio development process, including reflexivity, epistemological and ontological concerns and illustrate these considerations via three case studies. We show that, by expanding their methods portfolios, researchers will be better equipped to study the complex interactions shaping fisheries and contribute to solutions for sustainable fisheries management.

Small‐scale estimation of recreational fishing effort and catch from broad‐scale survey data: A case study using multiple‐use Marine Protected Areas in Western Australia

AbstractSustainability assessment and management evaluation of broad‐scale recreational fisheries are routinely informed using effort and catch data sourced from recurring offsite surveys. Similar information is often required for small‐scale recreational fisheries and other spatial management areas. Data from four state‐wide recreational fishing surveys in Western Australia were evaluated using grid‐ and location‐based direct estimation approaches to determine whether effort and total catch could be estimated robustly for small‐scale geographical areas. Marine protected areas (MPAs) were selected as case studies, and robustness of the various approaches was assessed based on acceptable sample size and uncertainty. Effort and total catch (number retained and released across all species) were robustly estimated for 19 MPAs. Total catch was also robustly estimated for 32 teleost species across multiple MPAs. Robust estimates were less likely for offshore MPAs than coastal MPAs, with lower sample sizes associated with greater distance from boat ramps and population centres. Grid‐based approaches were therefore generally more appropriate for offshore MPAs, while location‐based approaches were more appropriate for coastal MPAs. This study demonstrates how existing monitoring of broad‐scale recreational fisheries fulfils a need for similar data in small‐scale recreational fisheries, thereby allowing for the efficient use of resources that benefit fisheries management and conservation objectives.

An evaluation of information sharing schemes to identify what motivates fishers to share catch information

AbstractAvoiding unwanted catches and reducing discards is an important objective of fisheries management. Fishers can avoid unwanted catches to some extent by improving selectivity of their fishing operations. This can be achieved through technical measures and gear modifications but also by adjusting when and where fishing takes place. Having access to real-time information, as provided through information sharing within a fleet, can help fishers avoid unwanted catches. Yet, there often remains a reluctance to share catch information with others. This paper compiles information from 15 case study examples of existing information sharing schemes in fisheries throughout the world. We compare the structure and operation of each of these schemes and determine what motivated participants to join and share potentially sensitive catch information. While there is no one-size-fits-all approach to designing and implementing information sharing schemes in fisheries, this paper highlights how industry and stakeholder support is often important, and understanding the needs, concerns, and motivations of any group of fishers is fundamental in developing and expanding such approaches.

Common but differentiated rights and responsibilities in tuna fisheries management

AbstractThe UN Law of the Sea Convention (LOSC) and one of the implementing agreements of the Convention—the UN Fish Stocks Agreement (UNFSA)—mandates all states to cooperate in the management of highly migratory and straddling fish stocks. In doing so, the UNFSA specifies that the special requirements of developing states need to be taken into account. To date, except in the Western and Central Pacific Fisheries Commission (WCPFC), there is no formal mechanism to identify these differential responsibilities in tuna regional fisheries management organizations (RFMOs). Although some conservation and management measures exempt small‐scale and artisanal fishing vessels, power imbalances within RFMOs tend to favour the interests of more developed and larger distant water fishing nations over those of small developing coastal states. To facilitate the implementation of differentiated responsibilities as mandated in UNFSA, in this study we develop a three‐step framework that could be applied in the case of new conservation and management measure proposals. The framework has also been tested based on two developing countries and compared with a developed state in the Indian Ocean Tuna Commission and the adopted resolutions in 2019. To facilitate better transparency and equitable decision‐making processes across RFMOs, this framework could be adapted based on member states' fisheries management objectives and target and non‐target species.

A structured seabird population model reveals how alternative forage fish control rules benefit seabirds and fisheries.

Fisheries for forage fish may affect the survival and reproduction of piscivorous predators, especially seabirds. However, seabirds have evolved life history strategies to cope with natural fluctuations in prey and it is difficult to separate effects of fishing on seabirds from impacts of natural variability. To date, potential impacts of forage fisheries on seabirds have mainly been explored using ecosystem models that simplify seabird-forage-fish dynamics. We sought to explore how different forage fish harvest policies affect seabirds, accounting for structured population dynamics, life history specifics, and variation in forage fish dependencies across life stages; and how impacts vary across seabird and forage fish life histories. To explore these impacts, we developed an age-stage structured seabird model that incorporates seabird diet specialization, foraging behavior, and reproductive strategy, as well as different functional responses between prey availability and adult survival, juvenile survival, reproductive success, and breeder propensity. We parameterized this model for two contrasting seabird life histories: (1) a low fecundity, limited foraging range, diet specialist ("restricted"); and (2) a high fecundity, wide ranging, diet generalist ("flexible"). Each was paired with two different forage fish prey archetypes that were fished under various control rules. The restricted seabird population was expectedly less robust to constant fishing pressure than the flexible seabird, and this sensitivity was mainly due to functional response parameterization, rather than other life history parameters. Particularly, the restricted seabird was highly sensitive to the relationship between prey availability and adult survival but was not sensitive to the relationship between prey and reproductive success. An adaptive biomass-limit harvest rule for forage fish resulted in substantially higher seabird abundance compared to constant fishing across all scenarios, with minimal trade-offs to the fishery (depending on fishery management objectives). However, mechanisms governing the impact of the forage fish fishery on the seabird varied by forage fish type. Therefore, tailoring forage fish management strategies to forage fish life history can lead to mutually acceptable outcomes for fisheries and seabirds. If data or time are limited, an adaptive control rule is likely a safe bet for meeting seabird conservation objectives with limited impacts to fisheries.

Age estimation comparison between whole and thin-sectioned otoliths and pelvic fin-ray sections of long-lived lake trout, Salvelinus namaycush, from Great Bear Lake, Northwest Territories, Canada

Studies to determine precision and bias of both methods and age-readers are important to evaluate reliability of age data used for developing fisheries management objectives. We assessed within-reader, between-reader, and between-method precision (coefficient of variation, CV%) and bias of age estimations for long-lived lake trout, Salvelinus namaycush, from Great Bear Lake using three readers with different levels of experience. The assessment used independent age estimates (n = 3 per reader) from whole and transverse-sectioned otoliths (range = 1–67 years), and pelvic fin-ray sections (range = 3–26 years). We also examined between-method differences in assigned confidence scores. Within readers, age estimates from sectioned otoliths were more precise (2.6–3.0%) than whole (3.6–4.5%) otoliths. Between whole and sectioned otoliths, precision of age estimates was 5.4% and bias was low up to age 20. Age was typically under-estimated from whole otoliths compared to sections for fish ≥ 34 years. Increased reader confidence was correlated with greater precision and younger age estimates, particularly for whole otoliths, but less so for fin rays. Age was estimated with higher confidence from otolith sections than other methods. The least experienced reader estimated age with the lowest precision, and between-reader bias was evident among older ages. Age was consistently under-estimated and less precise from pelvic fins compared to sectioned otoliths, and are therefore an unsuitable non-lethal alternative. Sectioned otoliths revealed longevity was greater (67 years) than historically documented using whole otoliths (53 years) for these fish. Our findings contribute to those relying on otoliths or pelvic fin rays to estimate ages of long-lived lake trout populations, which are a key component of freshwater fauna in polar North America.

The status of climate change adaptation in fisheries management: Policy, legislation and implementation

AbstractClimate change is altering ecosystems and fisheries throughout the world's oceans, demanding climate‐adaptive governance for conserving and managing living marine resources. While in some regions fisheries management systems address wider ecosystem dynamics within management frameworks and decision‐making, which may facilitate resilience to climate change, there remains a shortfall in terms of directly incorporating climate change adaptation into fisheries management legislation and implementation. This review assesses the current state of implementation of climate change adaptation into fisheries management policies and legislation across 11 national case studies, based on government documents and the primary literature. The overarching goal is to understand the key elements and gaps in existing fisheries management policies and legislation in the context of climate change. Given recent reforms of fisheries management policies and/or legislation across the nations examined, political recognition of the need to address climate change adaptation in fisheries management appears to be increasing; albeit formal mandates of climate‐adaptation objectives in fisheries management are largely missing. Based on our review, recommendations for achieving climate‐adaptive fisheries management regimes are developed. Overall, this study will help to inform and broaden the scope of management approaches and tools to accelerate the move towards adaptive fisheries management that accounts for climate change impacts on fish stocks, fisheries and the societies that depend upon them.

Estimation of the spawning stock and recruitment relationship of Octopus vulgaris in Asturias (Bay of Biscay) with generalized depletion models: implications for the applicability of MSY

Abstract We developed a new type of generalized depletion model adapted to the rapid life cycle of Octopus vulgaris and the data collection framework put in place in its co-managed small-scale fishery (SSF) in Asturias, northwest Spain. The model uses weekly data from 19 seasons to estimate annual recruitment and female spawners emigration out of the vulnerable stock to attend to their broods. The matched annual spawners-recruitment (SR) magnitudes are then used as observations in a non-Bayesian hierarchical inference framework. The Shepherd SR model was selected among three alternatives. The stock has a high degree of density-dependence, leading to overcompensation. The estimated SR model has an unstable equilibrium point, driving the stock to deterministic cyclic fluctuations under small disturbances. Under those conditions the maximum sustainable yield (MSY) is not applicable, lending further credence to Sidney Holt’s opposition to the MSY as a basis for the elaboration of fishery management objectives, with potentially wide relevance to the management of SSF and cephalopod fisheries. We argue that harvest rates based on mean latent productivity, a concept that includes the MSY as a special case, are more adequate and sustainable for fluctuating stocks.

Grand challenge for habitat science: stage-structured responses, nonlocal drivers, and mechanistic associations among habitat variables affecting fishery productivity

Abstract Spatial management has been adopted worldwide to mitigate habitat impacts while achieving fisheries management objectives. However, there is little theory or practice for predicting the impact of spatial regulations on future fishery production; this would provide scientific basis for greater flexibility in fisheries management when balancing fishery and conservation goals. We propose that predicting changes in fishery production resulting from human activities within specific habitats is a “Grand Challenge” for habitat science in the coming decade(s). We then outline three difficulties in resolving this Grand Habitat Challenge, including: (i) stage-structured responses to habitat impacts, (ii) nonlocal responses, and (iii) mechanistic associations among habitat variables. We next discuss analytical approaches to address each difficulty, respectively: (i) ongoing developments for spatial demographic models; (ii) individual movement models and rank-reduction approaches to identify regional variability; (iii) causal analysis involving structural equation models. We demonstrate nonlocal effects in detail using a diffusion-taxis movement model applied to sablefish (Anoplopoma fimbria) in the Gulf of Alaska and discuss all three approaches for deep-sea corals. Despite isolated progress to resolve individual difficulties, we argue that resolving this Grand Habitat Challenge will require a coordinated commitment from science agencies worldwide.

The importance of biophysical context in understanding marine protected area outcomes for coral reef fish populations

Multiuse marine protected areas (MPAs) that utilize a mosaic of no-take and sustainable use zones are an increasingly common tool for promoting fish population recovery while minimizing socioeconomic conflict. However, significant gaps remain in our understanding of the effects of multiuse MPAs on reef-fish populations, and how protection from fishing may interact with biophysical gradients to drive ecological outcomes. Here, we examine changes in fish assemblages inside and outside of two multiuse MPAs in Raja Ampat, Indonesia, over the first four to five years after their implementation. We use linear models to assess the impact of protection status, anthropogenic pressure, and biophysical gradients on changes in four biological metrics: abundance, biomass, mean size, and size-spectra. In addition, we use multivariate analyses to assess whether fish assemblages in protected and unprotected reefs diverged after MPA establishment. We find that both fish abundance and biomass were driven equally or more by benthic characteristics than protection status and that these environmental impacts were decoupled from the effects of MPAs. Contrary to expectations, increases in abundance were more pronounced in unprotected reefs, where fish assemblages diverged from protected reefs through an increase of herbivorous parrotfishes (Subfamily Scarinae) likely driven by increased algal production on hard-bottom reef areas. However, mean size and size-spectra improved in sustainable use zones compared to unprotected reefs, demonstrating that non-exclusionary management can provide ecological benefits, especially when combined with nearby no-take areas. Increased mean size was also associated with lower human population sizes, suggesting a strong influence of fishing pressure, which is mediated by MPAs. Our findings suggest that multiuse MPAs can quickly achieve some fisheries management objectives and that these effects are likely to increase over longer timescales. However, biophysical context can have significant impacts on reef-fish assemblages that are distinct from the effects of overlying fisheries management.