Pelagic Forage Research Articles

Habitat selection and influence on hunting success in female Australian fur seals

Determining the factors influencing habitat selection and hunting success in top predators is crucial for understanding how these species may respond to environmental changes. For marine top predators, such factors have been documented in pelagic foragers, with habitat use and hunting success being linked to chlorophyll-a concentrations, sea surface temperature and light conditions. In contrast, little is known about the determinants of benthic marine predators. The Australian fur seal (Arctocephalus pusillus doriferus) is a benthic-diving forager that has a breeding and foraging distribution largely restricted to Bass Strait, the shallow (max. depth 80 m) continental shelf region between the Australian mainland and Tasmania. The species forages mostly on benthic prey and represents the greatest resident marine predator biomass in south-eastern Australia. The region is also one of the world’s fastest-warming marine areas and oceanographic changes are influencing shifts in prey distribution and abundance. In the present study, GPS-derived locations of benthic dives (n = 288,449) and dive behaviour metrics were used to determine seafloor habitat selection and factors influencing hunting success in 113 lactating adult females from Kanowna Island during the winters of 2006–2021. Individuals non-randomly selected foraging habitats comprised of deeper, steeper sloped, muddy-sandy areas with less gravel and highly disturbed regions (P < 0.01). Hunting success was greatest in shallower rocky reefs (< 30 m) and deep areas (> 40 m) characterised by moderate presence of gravel (25–50%) and substantial rock composition (50–75%) on the seabed. These findings suggest that habitat use and hunting success in adult female Australian fur seals could be impacted by predicted oceanographic changes, such as rising temperature, altered currents and waves which may modify seafloor characteristics and benthic communities.

Variability in coastal habitat available for Longfin Smelt Spirinchus thaleichthys in the northeastern Pacific Ocean

An understanding of oceanographic conditions and processes important to marine animal ecology is fundamental to the development of effective management and conservation actions. Longfin Smelt (Spirinchus thaleichthys) is a pelagic forage fish found in coastal and estuarine waters along the Pacific coast of North America from Alaska to central California. Substantial population declines in California’s San Francisco Estuary, where Longfin Smelt are protected under California’s Endangered Species Act, have prompted extensive study of estuarine factors associated with the decline. However, coastal factors that affect up to two-thirds of the Longfin Smelt life cycle are poorly understood and may be important drivers of population dynamics. We compiled coastal observations from numerous sources to estimate the range-wide coastal marine distribution of Longfin Smelt and assess habitat factors affecting distribution in the northeast Pacific Ocean. Based on maximum entropy species distribution models, Longfin Smelt distribution was correlated with depth, distance from the nearest estuary, sea surface temperature, and sea surface chlorophyll. Longfin Smelt were found in shallow, higher productivity coastal waters closer to estuaries, with depth and temperature the most consistent factors influencing distribution. Habitat suitability was highly variable at the southern extent of the range, particularly off the California coast, and was largely driven by habitat contractions associated with warm-water conditions. Study results provide insights into the habitat and range-wide distribution of an at-risk estuarine-reliant forage fish and are the first step toward identifying processes that affect the marine portion of the Longfin Smelt life cycle.

Evaluating robustness of harvest control rules to climate-driven variability in Pacific sardine recruitment

Climate-driven changes in ocean temperatures, currents, or plankton dynamics may disrupt pelagic forage fish recruitment. Being responsive to such impacts enables fisheries management to ensure continued sustainable harvest of forage species. We conducted a management strategy evaluation to assess the robustness of current and alternative Pacific sardine harvest control rules under a variety of recruitment scenarios representing potential projections of future climate conditions in the California Current. The current environmentally informed control rule modifies the harvest rate for the northern sardine subpopulation based on average sea surface temperatures measured during California Cooperative Oceanic Fisheries Investigations field cruises. This rule prioritizes catch at intermediate biomass levels but may increase variability in catch and closure frequency compared to alternative control rules, especially if recruitment is unrelated to ocean temperatures. Fishing at maximum sustainable yield and using dynamically estimated reference points reduced the frequency of biomass falling below 150 000 mt by up to 17%, while using survey index-based biomass estimates resulted in a 14% higher risk of delayed fishery closure during stock declines than when using assessment-based estimates.

Explicitly incorporating ecosystem-based fisheries management into management strategy evaluation, with a focus on small pelagics

The need to transition from traditional single-species fisheries management approaches towards ecosystem-based fisheries management (EBFM), or an ecosystem approach to fisheries, is widely recognised. EBFM is particularly important when considering management actions for economically valuable fisheries for small pelagic forage fish, given their key ecological role. Management strategy evaluation (MSE) is an effective approach to advance the quantitative implementation of EBFM by enabling stakeholders to explore trade-offs among competing ecosystem-related objectives. This paper puts forward six different approaches to advance EBFM with MSE explicity, by taking advantage of data and research already available and by guiding future research. These approaches can be grouped into those which (i) involve the operating model and/or link directly to the operating model while potentially providing additional performance metrics to evaluate ecosystem objectives, (ii) can be incorporated into the performance metrics, and (iii) involve the harvest control rule of the management procedure. This review demonstrates that immediate steps can be taken to implement EBFM targeted at quantitative tactical management, even without a complex, data-rich ecosystem operating model.

Assessing small pelagic fish trends in space and time using piscivore stomach contents

Changing distribution and abundance of small pelagic fishes may drive changes in predator distributions, affecting predator availability to fisheries and surveys. However, small pelagics are difficult to survey directly, so we developed a novel method of assessing the aggregate abundance of 21 small pelagic forage taxa via predator stomach contents. We used stomach contents collected from 22 piscivore species captured by multiple bottom trawl surveys within a vector autoregressive spatio-temporal model to assess trends of small pelagics on the Northeast US shelf. The goal was to develop a spatial “forage index” to inform survey and (or) fishery availability in the western North Atlantic bluefish ( Pomatomus saltatrix) stock assessment. This spatially resolved index compared favorably with more traditional design-based survey biomass indices for forage species well sampled by surveys. However, our stomach content-based index better represented smaller unmanaged forage species that surveys are not designed to capture. The stomach-based forage index helped explain bluefish availability to the recreational fishery for stock assessment and provided insight into pelagic forage trends throughout the regional ecosystem.

The potential of insects as alternative animal protein source for livestock feeding

The livestock industry as an important component of general agriculture is a key contributor to economic growth and development of any nation. In addition to having the capacity for earning revenue for the governments, it provides employment, food, farm energy, manure, fuel and transport. Currently, important protein ingredients for animal feed are fish meal, processed animal proteins and soybean meal. However, in the European Union the use of processed animal proteins in animal feed is prohibited due to the TSE legislation, globally land availability for soya cultivation is limited, while marine overexploitation has reduced the abundance of small pelagic forage fish from which fish meal and fish oil is derived. The growing scarcity of resources to produce these increasingly demanded ingredients has doubled prices during the last five years, while it already represents 60-70% of production costs. So, alternative (animal) protein sources for livestock and aquaculture are urgently needed.Insects are such an alternative animal protein source, which can sustainably reared on organic side streams. Reasons are that they have a favorable feed conversion efficiency, likely because they are cold-blooded. Insects contain between 30% and 70% protein on a dry matter basis. The protein content of the insect species is within the soybean/fish meal range and fat content is higher especially compared to (defatted) soybean meal. This review, however highlighted the environmental, health, livelihood and social benefits of insects. Recent efforts in feeding livestock, challenges limiting the use of insects as feed ingredients and moreover, the strategies for commercial production of insects as feed ingredients just to mention a few of the potentials of using insects for feeding livestock.

Diel vertical migration in Pacific sand lance (Ammodytes personatus)—a pelagic forage fish associated with benthic substrates

AbstractDiel vertical migration (DVM) in marine organisms is an evolved response to maximize foraging opportunities and minimize predation risk. This pattern in vertical distribution is a widely observed phenomenon and common in pelagic forage fish species. Modelling these dynamics has important relevance to understanding marine ecosystem dynamics, predator–prey interactions, and marine food webs. We examine DVM in sand lance—an ecologically important taxa of forage fishes throughout northern hemisphere marine systems and target of commercial fisheries. Much remains unknown about their diurnal emergence from sediments. We apply data from autonomous stereo-camera deployments and tank observations to provide new insight to DVM patterns in Pacific sand lance (Ammodytes personatus). We model emergence curves using beta regression models with random effects, depicting important differences in the shape of ascent and descent. Our observations and analyses document crepuscular movement patterns, suggesting pelagic foraging occurs primarily at dawn and dusk. Results suggest critical light thresholds are necessary to initiate and maintain pelagic foraging. Results also suggest the importance of seasonality and life stage, such that adult fish exhibit reduced pelagic foraging in the fall relative to juvenile fish. These results constitute a comprehensive evaluation of DVM in this species, better define the physical drivers, and mathematically depict the pattern and shape of emergence timing.

The role of conspecifics during pelagic foraging of Magellanic and benthic foraging of Gentoo penguins in the Beagle Channel, Argentina

The role of conspecifics during pelagic foraging of Magellanic and benthic foraging of Gentoo penguins in the Beagle Channel, Argentina

Energetic synchrony throughout the non‐breeding season in common guillemots from four colonies

The non‐breeding season presents significant energetic challenges to birds that breed in temperate or polar regions, with clear implications for population dynamics. In seabirds, the environmental conditions at non‐breeding sites drive food availability and the energetic cost of regulatory processes, resulting in variation in diet, behaviour and energetics; however, very few studies have attempted to understand if and how these aspects vary between populations. We investigated whether non‐breeding location influenced diet, behaviour and energetics in the common guillemotUria aalge. We studied guillemots from four UK breeding colonies, two located on the west coast of Scotland and two on the east. We quantified non‐breeding distribution, foraging behaviour and activity budgets of 39 individuals from July to March, using geolocation–immersion loggers and time‐depth recorders, and used feather stable isotope signatures to infer diet during the post‐breeding moult. We calculated energy expenditure and investigated whether the peak (an indicator of the potential vulnerability to marine threats) varied between colonies. Individuals were spatially segregated according to the coastline they breed on, with west coast guillemots distributed off the west coast of the UK and east coast guillemots distributed off the east coast. Diet and behaviour were more similar in guillemots that shared a breeding coastline than those that did not, as west coast guillemots foraged at a lower trophic level, spent less time diving and engaged in more pelagic foraging than east coast guillemots. However, energy expenditure was remarkably similar between colonies, peaking during late February/early March, indicating that, during our study period, there was high synchrony between colonies in the timing of potential vulnerability to marine threats. Therefore, any anthropogenic changes that result in decreased food availability or increased energy expenditure during late winter may have greater impacts on energy balance, with consequences for population dynamics.

Clustering and classification of vertical movement profiles for ecological inference of behavior

AbstractVertical movements can expose individuals to rapid changes in physical and trophic environments—for aquatic fauna, dive profiles from biotelemetry data can be used to quantify and categorize vertical movements. Inferences on classes of vertical movement profiles typically rely on subjective summaries of parameters or statistical clustering techniques that utilize Euclidean matching of vertical movement profiles with vertical observation points. These approaches are prone to subjectivity, error, and bias. We used machine learning approaches on a large dataset of vertical time series (N = 28,217 dives) for 31 post‐nesting leatherback turtles (Dermochelys coriacea). We applied dynamic time warp (DTW) clustering to group vertical movement (dive) time series by their metrics (depth and duration) into an optimal number of clusters. We then identified environmental covariates associated with each cluster using a generalized additive mixed‐effects model (GAMM). A convolutional neural network (CNN) model, trained on standard dive shape types from the literature, was used to classify dives within each DTW cluster by their shape. Two clusters were identified with the DTW approach—these varied in their spatial and temporal distributions, with dependence on environmental covariates, sea surface temperature, bathymetry, sea surface height anomaly, and time‐lagged surface chlorophyll a concentrations. CNN classification accuracy of the five standard dive profiles was 95%. Subsequent analyses revealed that the two clusters differed in their composition of standard dive shapes, with each cluster dominated by shapes indicative of distinct behaviors (pelagic foraging and exploration, respectively). The use of these two machine learning approaches allowed for discrete behaviors to be identified from vertical time series data, first by clustering vertical movements by their movement metrics (DTW) and second by classifying dive profiles within each cluster by their shapes (CNN). Statistical inference for the identified clusters found distinct relationships with environmental covariates, supporting hypotheses of vertical niche switching and vertically structured foraging behavior. This approach could be similarly applied to the time series of other animals utilizing the vertical dimension in their movements, including aerial, arboreal, and other aquatic species, to efficiently identify different movement behaviors and inform habitat models.

Using predator diets to infer forage fish distribution and assess responses to climate variability in the eastern Bering Sea

Forage fishes comprise an integral part of marine food webs in the highly productive ecosystems of the North Pacific. However, significant knowledge gaps exist related to the status of forage fish, their life histories, and how populations may react to future climatic shifts. Standardized bottom trawl surveys are critical to the stock assessment of groundfish but lack the gear and protocols to quantitatively evaluate small pelagic forage fish. Where diet data are available, predators may be used as an indirect method of collecting data on forage fish distribution and relative abundance. We used stomach contents data to infer predator-prey interactions in the eastern Bering Sea and to analyze the distribution of 5 forage taxa over a 34 yr time series (1985-2019). Using 4 dominant groundfish predators, we constructed forage fish and predator depth and temperature habitat profiles and used center of gravity (COG) analysis and global index of collocation to examine predator-prey overlap. Results provide insight on the habitat partitioning and competitive interactions between forage species and the dynamics between predators and prey. Interannual COG analyses indicated recent periods of cooling (2007-2013) and warming (2014-2019) had significant effects on the distribution of forage fish, and suggest differences in the relative resilience of forage fish populations to climate change in this region. Population shifts were particularly evident in recent periods of anomalous warming, highlighting the need to understand how future periods of prolonged warming may affect predator-prey dynamics. Results also demonstrate the importance of predator diet time series and how these data might inform multi-species models and management strategies.

Multi-colony tracking reveals segregation in foraging range, space use, and timing in a tropical seabird

Colonial animals experience density-dependent competition for food, which is posited to influence foraging range and lead to inter-colony segregation. However, such patterns are poorly studied in the tropics, where predictable day lengths, oligotrophic conditions, and facultative foraging may alter the relationships between foraging and intra-specific competition. Here, we GPS-tracked 207 breeding red-footed boobies Sula sula rubripes (RFB) from 4 neighbouring Chagos Archipelago colonies (~1100 to 9200 breeding pairs) in the central Indian Ocean, to determine how foraging strategies (i.e. effort, segregation, and timing) vary with colony, while accounting for sex, monsoon season, stage of reproduction, year, and individual. During incubation and chick-rearing, RFBs commute to pelagic foraging grounds (maximum distance mean ± SE: 112.9 ± 3.7 km; total distance: 298.4 ± 6.2 km) over 1 to 5 d (18.5 ± 1.6 h). Foraging effort was highest at the largest colony, and greater among females than males. Departure angles varied among colonies, leading to foraging areas that were largely spatially segregated. Timing of departures and arrivals were strongly constrained by daylight hours, although females and birds at the largest colony left earliest. Our study highlights the importance of inter-colony differences in tropical seabird foraging, which may relate to different levels of intra-specific competition. Moreover, links between foraging times and colony size suggest a previously undescribed outcome of density-dependent competition, highlighting the importance of understanding colonial living across multiple dimensions.

Energetic consequences of resource use diversity in a marine carnivore.

Understanding how intraspecific variation in the use of prey resources impacts energy metabolism has strong implications for predicting long-term fitness and is critical for predicting population-to-community level responses to environmental change. Here, we examine the energetic consequences of variable prey resource use in a widely distributed marine carnivore, juvenile sand tiger sharks (Carcharias taurus). We used carbon and nitrogen isotope analysis to identify three primary prey resource pools-demersal omnivores, pelagic forage, and benthic detritivores and estimated the proportional assimilation of each resource using Bayesian mixing models. We then quantified how the utilization of these resource pools impacted the concentrations of six plasma lipids and how this varied by ontogeny. Sharks exhibited variable reliance on two of three predominant prey resource pools: demersal omnivores and pelagic forage. Resource use variation was a strong predictor of energetic condition, whereby individuals more reliant upon pelagic forage exhibited higher blood plasma concentrations of very low-density lipoproteins, cholesterol, and triglycerides. These findings underscore how intraspecific variation inresource use may impact the energy metabolism of animals, and more broadly, that natural and anthropogenically driven fluctuations in prey resources could have longer term energetic consequences.

Evolutionary divergence in phenotypic plasticity shapes brain size variation between coexisting sunfish ecotypes.

Mechanisms that generate brain size variation and the consequences of such variation on ecological performance are poorly understood in most natural animal populations. We use a reciprocal-transplant common garden experiment and foraging performance trials to test for brain size plasticity and the functional consequences of brain size variation in Pumpkinseed sunfish (Lepomis gibbosus) ecotypes that have diverged between nearshore littoral and offshore pelagic lake habitats. Different age-classes of wild-caught juveniles from both habitats were exposed for 6 months to treatments that mimicked littoral and pelagic foraging. Plastic responses in oral jaw size suggested that treatments mimicked natural habitat-specific foraging conditions. Plastic brain size responses to foraging manipulations differed between ecotypes, as only pelagic sourced fish showed brain size plasticity. Only pelagic juveniles under 1year-old expressed this plastic response, suggesting that plastic brain size responses decline with age and so may be irreversible. Finally, larger brain size was associated with enhanced foraging performance on live benthic but not pelagic prey, providing the first experimental evidence of a relationship between brain size and prey-specific foraging performance in fishes. The recent post-glacial origin of these ecotypes suggests that brain size plasticity can rapidly evolve and diverge in fish under contrasting ecological conditions.

Relative exposure to microplastics and prey for a pelagic forage fish

In the global ocean, more than 380 species are known to ingest microplastics (plastic particles less than 5 mm in size), including mid-trophic forage fishes central to pelagic food webs. Trophic pathways that bioaccumulate microplastics in marine food webs remain unclear. We assess the potential for the trophic transfer of microplastics through forage fishes, which are prey for diverse predators including commercial and protected species. Here, we quantify Northern Anchovy (Engraulis mordax) exposure to microplastics relative to their natural zooplankton prey, across their vertical habitat. Microplastic and zooplankton samples were collected from the California Current Ecosystem in 2006 and 2007. We estimated the abundance of microplastics beyond the sampled size range but within anchovy feeding size ranges using global microplastic size distributions. Depth-integrated microplastics (0–30 m depth) were estimated using a depth decay model, accounting for the effects of wind-driven vertical mixing on buoyant microplastics. In this coastal upwelling biome, the median relative exposure for an anchovy that consumed prey 0.287–5 mm in size was 1 microplastic particle for every 3399 zooplankton individuals. Microplastic exposure varied, peaking within offshore habitats, during the winter, and during the day. Maximum exposure to microplastic particles relative to zooplankton prey was higher for juvenile (1:23) than adult (1:33) anchovy due to growth-associated differences in anchovy feeding. Overall, microplastic particles constituted fewer than 5% of prey-sized items available to anchovy. Microplastic exposure is likely to increase for forage fishes in the global ocean alongside declines in primary productivity, and with increased water column stratification and microplastic pollution.

Tidal streams, fish, and seabirds: Understanding the linkages between mobile predators, prey, and hydrodynamics

AbstractDriven by the necessity to decarbonize energy sources, many countries are targeting tidal stream environments for power generation. However, these areas can act as foraging hotspots for marine top predators, such as seabirds. Thus, it is important to understand the ecological interactions influencing predator behavior and distribution in these areas, to determine the potential ecological implications of marine renewable devices. This study used concurrent observations of foraging seabirds, physical hydrodynamics, and prey presence across a tidal stream environment, before and after the installation of a commercial turbine array close to the island of Stroma, Scotland. There were three main findings: First, benthic foraging seabirds showed a clear preference for certain sections around Stroma where sandeels were detected, while pelagic foraging seabirds were seen all around Stroma. Second, there was a positive effect of water velocity on the number of pelagic foragers and common guillemots. Third, there was a positive effect of the presence of fish schools on the number of pelagic seabirds and common guillemots, in both the same and the previous transects. Thus, it is possible that seabirds target areas of predictable food sources during periods where prey might be easily accessed (e.g., periods of fast flows). Given the difference in the distribution between seabird categories, it is likely that marine renewable devices will impact each category differently. We conclude that any impact on sandbank locations, sandeels preferred habitat, due to the presence of tidal turbines is likely to alter the distribution of benthic foraging seabirds. For pelagic foraging seabirds and common guillemot, changes in prey presence and accessibility (depth and level of aggregation/disaggregation) will have a stronger effect on seabird presence. This study highlights the need to include concurrent physical and biological data when assessing the ecological impacts of tidal turbines.

A stable foraging polymorphism buffers Galápagos sea lions against environmental change

Understanding the ability of animals to cope with a changing environment is critical in a world affected by anthropogenic disturbance.1 Individual foraging strategies may influence the coping ability of entire populations, as these strategies can be adapted to contrasting conditions, allowing populations with foraging polymorphisms to be more resilient toward environmental change.2,3 However, environmentally dependent fitness consequences of individual foraging strategies and their effects on population dynamics have not been conclusively documented.4,5 Here, we use biologging data from endangered Galápagos sea lion females (Zalophus wollebaeki) to show that benthically foraging individuals dig after sand-dwelling prey species while pelagic foragers hunt in more open waters. These specialized foraging behaviors result in distinct and temporally stable patterns of vibrissae abrasion. Using vibrissae length as a visual marker for the benthic versus pelagic foraging strategies, we furthermore uncovered an environment-dependent fitness trade-off between benthic and pelagic foragers, suggesting that the foraging polymorphism could help to buffer the population against the negative effects of climate change. However, demographic projections suggest that this buffering effect is unlikely to be sufficient to reverse the ongoing population decline of the past four decades.6 Our study shows how crucial a deeper understanding of behavioral polymorphisms can be for predicting how populations cope within a rapidly changing world. VIDEO ABSTRACT.

Pelagic forage versus abiotic factors as drivers of walleye growth in northern Wisconsin lakes

Pelagic forage versus abiotic factors as drivers of walleye growth in northern Wisconsin lakes

Tradeoffs of managing cod as a sustainable resource in fluctuating environments.

Sustainable human exploitation of living marine resources stems from a delicate balance between yield stability and population persistence to achieve socioeconomic and conservation goals. But our imperfect knowledge of how oceanic oscillations regulate temporal variation in an exploited species can obscure the risk of missing management targets. We illustrate how applying a management policy to suppress fluctuations in fishery yield in variable environments (prey density and regional climate) can present unintended outcomes in harvested predators and the sustainability of harvesting. Using Atlantic cod (Gadus morhua, an apex predatory fish) in the Barents Sea as a case study we simulate age-structured population and harvest dynamics through time-varying, density-dependent and density-independent processes with a stochastic, process-based model informed by 27-year monitoring data. In this model, capelin (Mallotus villosus, a pelagic forage fish), a primary prey of cod, fluctuations modulate the strength of density-dependent regulation primarily through cannibalistic pressure on juvenile cod survival; sea temperature fluctuations modulate thermal regulation of cod feeding, growth, maturation, and reproduction. We first explore how capelin and temperature fluctuations filtered through cod intrinsic dynamics modify catch stability and then evaluate how management to suppress short-term variability in catch targets alters overharvest risk. Analyses revealed that suppressing year-to-year catch variability impedes management responses to adjust fishing pressure, which becomes progressively out of sync with variations in cod abundance. This asynchrony becomes amplified in fluctuating environments, magnifying the amplitudes of both fishing pressure and cod abundance and then intensifying the density-dependent regulation of juvenile survival through cannibalism. Although these transient dynamics theoretically give higher average catches, emergent, quasicyclic behaviors of the population would increase long-term yield variability and elevate overharvest risk. Management strategies that overlook the interplay of extrinsic (fishing and environment) and intrinsic (life history and demography) fluctuations thus can inadvertently destabilize fish stocks, thereby jeopardizing the sustainability of harvesting. These policy implications underscore the value of ecosystem approaches to designing management measures to sustainably harvest ecologically connected resources while achieving socioeconomic security.

Changes in Habitat Conditions, Fish Populations, and the Fishery in Northern Green Bay, Lake Michigan, 1989–2019

AbstractAquatic environments and biological communities in nearshore waters of the Laurentian Great Lakes have undergone extensive change in recent decades. The nearshore waters of northern Green Bay, Lake Michigan, have been subject to environmental change but are relatively unstudied, despite hosting important fisheries for Walleye Sander vitreus, Yellow Perch Perca flavescens, Northern Pike Esox lucius, and Smallmouth Bass Micropterus dolomieu. Our objectives were to (1) test for changes in water clarity and fish populations in northern Green Bay, Lake Michigan, during 1989–2019, (2) depict recent spatial patterns in abundance for species of management interest, and (3) test for effects of recent Great Lakes water level changes on Northern Pike recruitment. Fishes were sampled annually in August and September 1989–2019 via trawl and gill‐net surveys at index sites. Mean water clarity increased 30% over this period. Aside from Round Goby Neogobius melanostomus, total catch rate of species in trawls decreased by over 90% between the 1990s and 2010s, with significant declines for Yellow Perch and pelagic forage fishes (coincident with dreissenid mussel invasion). Fish species richness in trawl and gill‐net surveys and total gill‐net catch rates declined significantly over time. Trends in gill‐net catch rates of game fishes during 1989–2019 were species‐specific, with spatial patterns often related to availability of preferred habitat conditions. Similar fish community changes to those we observed in northern Green Bay, Lake Michigan, have been noted in other Great Lakes, many being associated with invasion of dreissenid mussels and Round Goby. Increased water levels in Lake Michigan during the 2010s had a significant positive effect on Northern Pike recruitment, which highlights the importance of varying water levels, shoreline habitat conditions, and early life processes on population dynamics of fishes reproducing in inshore habitats.