Oyster Reef Habitat Research Articles

Estuarine nekton community shows minimal response following large-scale oyster reef habitat loss in Apalachicola Bay, Florida

Estuarine nekton community shows minimal response following large-scale oyster reef habitat loss in Apalachicola Bay, Florida

Nitrogen-cycling genes in oyster reefs and surrounding sediments: Relationships with environmental factors and respective nitrogen rates

To investigate nitrogen (N) cycling in oyster reef habitats along the East coast of Australia, we assessed N-cycling gene abundances in oyster shell biofilms and surrounding sediments, and explored their correlation with environmental factors and respective N rates. We found higher abundances of the denitrification gene nosZII in oyster shell biofilms, while there were not significant differences in the denitrification genes nirS and nirK between oyster biofilms and sediments. Additionally, oyster shell biofilms had a lower (nirS + nirK)/nosZII ratio, indicating a greater capacity for N removal and limited nitrous oxide release compared to sediments. Abundance of nirS, nirK, and dissimilatory nitrate reduction to ammonium (nrfA) genes in sediments decreased with increasing content of organic material, suggesting the influence of large-scale environmental conditions. N-cycling gene abundances did not relate to N rates, emphasising the importance of investigating microbial genes to enhance our understanding of the N cycle in oyster reef habitats.

Evidence of ontogenetic partitioning of restored coastal habitat by a generalist sportfish

Coastal and estuarine habitats that provide crucial nursery areas for many economically and ecologically important fish species are in decline. Restoration of benthic habitats can improve fish populations, biomass, and feeding opportunities, but there is limited research on how restoration impacts growth and survival with ontogeny. To address this knowledge gap, here we examine the biometrics (size, biomass, and body condition), recruitment, size structure, and trophic shifts of a sportfish (mangrove snapper, Lutjanus griseus) at restored oyster reefs and stabilized living shorelines to better understand how fish use restored habitats as they grow. Biomass and body condition of L. griseus juveniles and subadults, and post‐settlement recruitment, at restored/stabilized sites was similar, and in some cases greater than natural sites, correlating with benthic habitat, reef location, and lunar phase at oyster reefs. Living shorelines exhibited greater recruitment potential, while oyster reefs supported more juveniles and subadults, as evidenced by differences in fish size and biomass between habitats. Dietary overlap implies subadult L. griseus likely foraged across habitats more than juveniles, while there was greater diet similarity within habitats. Furthermore, ontogenetic shifts also occurred within oyster reef habitats, highlighting the importance of quality habitat to support various sportfish life stages, which can be achieved through restoration. These findings suggest life history attributes can be indicators of habitat restoration success, and specifically provide actionable science to guide the development of more effective strategies for restoring inshore nursery habitats and thus augment production of offshore reef fisheries.

First-Year Performance of the Pervious Oyster Shell Habitat (POSH) along Two Energetic Shorelines in Northeast Florida

Novel living shoreline methods are being developed to minimize negative environmental impact while maintaining strength and effectiveness in high-energy systems. The “Pervious Oyster Shell Habitat” (POSH) is a novel structure composed of oyster shells bound by a thin layer of Portland cement into the shape of a dome. The structure’s makeup greatly reduces its environmental impact while providing optimal substrate for the provision of oyster reef habitat. Previous laboratory testing has demonstrated that the structure is robust, and this follow-up study assesses the structure’s performance in the estuarine environment. Oyster and barnacle densities were compared between POSH modules and the industry standard “Oyster Ball” model Reef BallTM along two energetic shorelines in northeast Florida. Oyster densities on the POSH were high and significantly greater than on the Oyster Ball at both sites. Barnacle densities did not differ between structures and did not appear to affect oyster recruitment. The size distribution of oysters on POSH and Oyster Ball modules was measured to assess the demographics and growth of oysters over time. Overall, demographics were similar among the two structures. Differences in oyster densities and demographics were greater at our more energetic site. Results show that the POSH can be an optimal structure for early oyster recruitment and reef development in energetic systems and should be considered by restoration stakeholders.

Site selection for European native oyster (Ostrea edulis) habitat restoration projects: An expert‐derived consensus

Abstract The European native oyster (Ostrea edulis) is a threatened keystone species which historically created extensive, physically complex, biogenic habitats throughout European seas. Overfishing and direct habitat destruction, subsequently compounded by pollution, invasive species, disease, predation and climate change have resulted in the functional extinction of native oyster habitat across much of its former range. Although oyster reef habitat remains imperilled, active restoration efforts are rapidly gaining momentum. Identifying appropriate sites for habitat restoration is an essential first step in long‐term project success. In this study, a three‐round Delphi process was conducted to determine the most important factors to consider in site selection for European native oyster habitat restoration projects. Consensus was reached on a total of 65 factors as being important to consider in site selection for European native oyster habitat restoration projects. In addition to the abiotic factors typically included in habitat suitability models, socio‐economic and logistical factors were found to be important. Determining the temporal and spatial variability of threats to native oyster habitat restoration and understanding the biotic factors present at a proposed restoration site also influence the potential for project scale‐up and longevity. This list guides site selection by identifying: a shortlist of measurable factors which should be considered; the relevant data to collect; topics for discussion in participatory mapping processes; information of interest from the existing body of local ecological knowledge; and factors underpinning supportive and facilitating regulatory frameworks.

Oyster reef habitat depends on environmental conditions and management across large spatial scales

Oyster reefs provide important services to ecosystems and people, with many of these benefits depending on structurally complex reef habitat. Despite the key role of oyster reef habitat, we have yet to understand natural and anthropogenic drivers of subtidal reef habitat over large spatial scales (>200 km). Chesapeake Bay (USA) offers a valuable system to explore how salinity, restoration, and harvest compare in their influence on subtidal oyster reef habitat because of its broad environmental gradient and mosaic of management types. We applied a remote rapid assessment method using underwater photographs to survey oyster reef habitat in 12 tributaries and scored images based on estimates of oyster percent cover and vertical relief. The broad spatial scale (~215 km) of the survey includes reefs that vary in management status and salinity. Bay-wide habitat scores were higher with greater estimated oyster percent cover and vertical relief on unharvested and restored reefs. Salinity also contributed to Chesapeake Bay-wide patterns, but the relationship depended on harvest status. In assessing the separate management jurisdictions, scores were higher on restored reefs in Maryland and on anthropogenic (i.e. artificially supplemented) reefs in Virginia. A time series over 4 yr in 2 Maryland tributaries showed high and persistent habitat scores in restored sanctuaries, but habitat scores increased for all reefs over time. The results highlight the combined roles of the natural environment and management decisions on oyster reef habitat. The effect of harvest and restoration on habitat underscores the importance of local management decisions in determining the future status of oyster reefs.

Using Drone Imagery to Map Intertidal Oyster Reefs along Florida’s Gulf of Mexico Coast

Eastern oyster (Crassostrea virginica) reefs offer vital ecosystem services and support economically and culturally important fisheries. However, environmental and anthropogenic stressors have led to significant decline in oyster reef coverage globally and locally in places like the Suwannee Sound in Florida, USA. Current monitoring methods are insufficient for timely and accurate assessment of oyster resources in the region. Here we demonstrate how drone imagery can be used to delineate intertidal oyster reef coverage rapidly and reliably. The high spatial resolution offered by drone imagery enables accurate delineations. We use a segmentation algorithm to delineate reefs, which produces consistently detailed outlines that are more representative of reef morphology than manual delineations. In total, 1,394 reefs were delineated, which corresponds with 497, 670 m2 of reef area. Of the delineated reefs, 236 (17%) were newly mapped, aligning with 19,848 m2 of newly mapped intertidal oyster reef habitat. The overlapping drone imagery also enabled the production of digital surface models, which were used to calculate volume to area ratio as an indicator of reef condition. These delineations and features serve as accurate baseline data that can be compared to future surveys to monitor how reefs are changing over time in the Suwannee Sound. These methods can also be expanded to other geographical areas and can aid in identifying early signs of decline in oyster reefs.

Underwater Video as a Tool to Quantify Fish Density in Complex Coastal Habitats

Habitat loss is a serious issue threatening biodiversity across the planet, including coastal habitats that support important fish populations. Many coastal areas have been extensively modified by the construction of infrastructure such as ports, seawalls, docks, and armored shorelines. In addition, habitat restoration and enhancement projects often include constructed breakwaters or reefs. Such infrastructure may have incidental or intended habitat values for fish, yet their physical complexity makes quantitatively sampling these habitats with traditional gears challenging. We used a fleet of unbaited underwater video cameras to quantify fish communities across a variety of constructed and natural habitats in Perdido and Pensacola Bays in the central northern Gulf of Mexico. Between 2019 and 2021, we collected almost 350 replicate 10 min point census videos from rock jetty, seawall, commercial, public, and private docks, artificial reef, restored oyster reef, seagrass, and shallow sandy habitats. We extracted standard metrics of Frequency of Occurrence and MaxN, as well as more recently developed MeanCount for each taxon observed. Using a simple method to measure the visibility range at each sampling site, we calculated the area of the field of view to convert MeanCount to density estimates. Our data revealed abundant fish assemblages on constructed habitats, dominated by important fisheries species, including grey snapper Lutjanus griseus and sheepshead Archosargus probatocephalus. Our analyses suggest that density estimates may be obtained for larger fisheries species under suitable conditions. Although video is limited in more turbid estuarine areas, where conditions allow, it offers a tool to quantify fish communities in structurally complex habitats inaccessible to other quantitative gears.

A Resident Fish Guild as a Higher Trophic Level Indicator of Oyster Reef Restoration Success

Eastern oysters (Crassostrea virginica) are critical foundation species in estuarine waters, but due to a combination of natural and anthropogenic pressures, oyster abundance has declined. Restoring oyster reefs and monitoring restoration success often focuses on oyster metrics, but relatively infrequently, responses of higher trophic level species and the production of related ecosystem services are accounted for. To address this, we compare the response of a resident reef fish guild (gobies, blennies, toadfish) to standard metrics of oyster restoration success. Using lift nets and seines, natural and restored reefs were monitored over a two-year period within Mosquito Lagoon, Florida, USA. Standard metrics are indicative of restoration success; live oyster density and reef thickness increased in restored reefs after 12 and 24 months. Combined, live oyster density and reef thickness were the best predictors of annual resident reef fish abundance compared to water quality metrics. These results suggest that the benefits of restoring oyster reef habitat are conferred to broader components of the food web, with benefits accruing to reef resident fishes that are a key trophic linkage between lower trophic level foundation species and higher trophic level predators inhabiting coastal ecosystems.

Recruitment enhancement varies by taxonomic group and oyster reef habitat characteristics.

The rapid loss of coastal and estuarine biogenic habitats has reduced the delivery of valuable ecosystem services, resulting in calls for increased habitat restoration. Yet, a lack of information on how key habitat characteristics (e.g., area, vertical relief, age) influence the ability of restored habitats to deliver these ecosystem services hinders efforts to maximize the return on restoration investments. We conducted a meta-analysis to assess the influence of reef type (natural or restored), taxa, and restored reef size, vertical relief, age, and tidal zone on the presence and magnitude of recruitment enhancement for nekton (i.e., fish and swimming crabs). Both intertidal and subtidal reefs, as well as restored and natural reefs, enhanced nekton recruitment, though there was variation among taxonomic groups with reef types. Recruitment enhancement was more common across taxa on restored (six families) than on natural (one family) reefs. Resident nekton families were more consistently enhanced than transient families. Nekton enhancement varied with a number of restored reef characteristics. Recruitment enhancement increased with greater reef size across taxa, decreased with higher vertical relief for two families, showed maximum recruitment around a single intertidal reef age for one family, and showed minimum recruitment around a single subtidal reef age for three families. Understanding variation across species in response to key design elements will improve restoration success and enhance return on investment. Moving forward, we recommend studies that vary reef habitat characteristics independently and in combination to identify how variation in these characteristics interact to influence nekton recruitment enhancement by oyster reefs.

Genetic structure and effective population size of Sydney rock oysters in eastern Australia

Oyster reef habitats are critical to coastal biodiversity and their decline has prompted restoration efforts in Australia. Knowledge gaps exist regarding the population structure and diversity of key species in these habitats. This may be critical information for the design of effective restoration programs. Sydney rock oysters (Saccostrea glomerata) are the dominant reef-forming bivalve in eastern Australia. Wild populations of S. glomerata have declined due to overharvesting, disease outbreaks, coastal development and reduced water quality. Here, we use genetic markers identified by genome-wide sequencing to investigate the genetic structure and diversity of wild Sydney rock oysters throughout their distribution in eastern Australia. We examine evidence for past population bottlenecks and spatial genetic structure associated with the East Australian Current. Analysis of 3, 400 neutral single-nucleotide polymorphisms (SNPs) revealed a single population, and an overlap with two other Saccostrea sp. at the northernmost boundary of the distribution. We detected signals of asymmetric gene flow consistent with the direction of the East Australian Current, and spatial structure patterns of limited genetic isolation by distance and spatial autocorrelation in the northern region (which experiences stronger effects of the East Australian Current) but not in the southern region of the distribution. We found no evidence of significant recent bottlenecks, with high effective population size throughout the species’ range. This information will provide a baseline against which to assess the impact of restoration projects, and guide strategies for sourcing stock for the enhancement of wild oyster populations. Our results provide a positive outlook for the resilience and adaptive capacity of Sydney rock oysters, and highlight wild populations as valuable resources for aquaculture and restoration initiatives.

Saved by the shell: Oyster reefs can shield juvenile blue crabs Callinectes sapidus

Juvenile blue crabs Callinectes sapidus use seagrass and other structured habitats as refuges from predation. Oyster reef habitats provide structural complexity that may offer refuge, but the value of these habitats for juvenile blue crabs has not been examined. We quantified survival of juvenile C. sapidus in structured oyster reef habitat versus unstructured soft-bottom habitat. In a field tethering experiment in the York River, lower Chesapeake Bay (USA), juvenile C. sapidus (10-50 mm carapace width [CW]) were tethered in sand (n = 40) or oyster reef (n = 39) habitats at subtidal sites 1-2 m deep. An underwater camera system was used to record predation activity during 24 h trials. Juvenile crab survival was significantly higher on the oyster reef habitat (53.8%) than on bare sand (15.0%), and tended to increase with crab CW in both habitats. The main successful predators on juvenile blue crabs were northern pufferfish Sphoeroides maculatus in the oyster reef habitat and adult blue crabs in the sand habitat. The high survival rate of juvenile C. sapidus in oyster reef habitats suggests that oyster reefs include physical habitat complexity that may offer refuge from predators. Restored and natural oyster reefs could provide an alternative nursery habitat for juvenile blue crabs, expanding the ecosystem services provided by restored oyster reefs.

Rapid video assessment detects qualitative differences in oyster reef habitat

A combination of anthropogenic stressors and overharvesting has led to a loss of oyster reefs and the important ecosystem services they provide. Addressing these losses through restoration is now a focus of coastal and estuarine conservation efforts. The present study tested a low-cost, qualitative rapid assessment approach for monitoring habitat characteristics of subtidal oyster reefs differing in restoration activity. The study was conducted in 4 tributaries of the Choptank River complex, Maryland, USA, which included harvest areas and no-take reserves (sanctuaries). At each site, a categorical score ranging from 0 to 3 was compared with percent cover of oyster shell and of fouling organisms. Restored reefs in oyster sanctuaries had higher scores (2 to 3) and percent cover of oyster shell and fouling organisms than unrestored sanctuary reefs or reefs open to harvest; higher scores were also associated with greater percent cover of hard substrate and fouling organisms. The Harris Creek sanctuary reef system had the highest percentage of scores of 3 (40%), followed by tributaries with partially restored reef systems (14% in Little Choptank, 6% in Tred Avon) and harvest areas (2% in Broad Creek). Although validation with metrics of live oysters is needed, rapid video assessment appears to be an effective, low-cost tool for qualitative monitoring of subtidal oyster reefs in areas with adequate visibility.

Seasonal analysis of artificial oyster reef ecosystems: implications for sustainable fisheries management

Oyster reef habitats in estuarine areas are an important marine ecosystem globally. Due to the destruction of oyster reef habitats within the Luanhe River estuarine area, Bohai Sea, China, a local fisheries company created 2 km2 of artificial oyster reef habitats by deploying artificial reef blocks that provided a settling surface for a natural oyster population and conducted sea cucumber aquaculture. The aims of this study are to help fisheries managers to understand whether the ecosystem function of created oyster reef habitat is consistent throughout the seasons and to assess if the current fishing production policy which varies with seasons is reasonable. We presented steady-state trophic models in different seasons of a newly created artificial coastal oyster reef within the Luanhe River estuary to address the above issues. We concluded that seasonality is an important factor that needs to be carefully considered in the fisheries management of oyster reef ecosystems.

Densities of Large Marine Gastropods in Seagrass, Oyster Reef, and Sandy Habitats in Tampa Bay and along the Gulf Coast of Florida

Marine gastropods in Florida are harvested by the marine-life trade, tourists (for shells), and traditional commercial fisheries, but stocks are not formally assessed for most species. The main goal of this project was to estimate biological variables that may be used to evaluate the Species of Greatest Conservation Need status of the banded tulip Cinctura lilium and six other large marine gastropod species that are commonly encountered in the targeted habitats. The principal target, C. lilium, was listed in the 2012 State Wildlife Action Plan. The densities and size structures of C. lilium and six co-occurring species of large marine gastropods in Tampa Bay were examined to evaluate population dynamics, seasonal variation, and habitat preferences of these species. Long-term trends in the densities of large, predatory marine gastropods in 10 regions from 2009 to 2017 were included. In Tampa Bay, strong habitat preferences were observed for all species studied: C. lilium and Melongena corona were most likely to be observed on oyster reefs, and Fasciolaria tulipa was found only in seagrass, whereas Strombus alatus, Triplofusus gigantea, Sinistrofulgur sinistrum, and Fulguropsis spirata were more common on soft sediments. Seasonal variations in densities were weak; seasonal differences in size structure were more pronounced. The smallest individuals of C. lilium appeared in spring and summer; F. spirata, S. alatus, and S. sinistrum reached a detectable size in fall. The smallest detectable M. corona appeared in winter. Regionally, there were more gastropods in southwestern bay grass beds (Tampa Bay, Sarasota Bay, and Pine Island Sound) than in coastal seagrass beds (Big Bend, Citrus, Hernando, Pasco, and coastal Pinellas) or northern bays (St. Joseph Bay and St. Andrew Bay), and each region had characteristic species. As a group, tulip snails exhibited modest local declines in densities at two sites, whereas the whelks and T. gigantea varied annually but did not exhibit consistent trends during 2009 to 2017. The present study establishes a baseline of abundance for seven species of common marine gastropods and recommends expanded monitoring in multiple habitats to improve future analyses of abundance trends.

Alternative Substrates Used for Oyster Reef Restoration: A Review

Oyster populations and reef habitats have notably declined in the last century around the world. The ecological, economic, and cultural values of oysters have led to a variety of restoration efforts seeking to recover these lost benefits. Limitations of the native oyster shell substrate and the large-scale nature of many restoration projects have resulted in the increased use of a variety of alternative, or artificial, substrates to create reef structures. A text mining package was used to conduct a review of alternative substrates used for oyster restoration. Specifically, the review (1) assessed commonly used alternative substrates, (2) locations where alternative substrates are used, and (3) common performance metrics used to evaluate alternative substrates. The review demonstrated that (1) the most common substrates included porcelain, concrete, limestone, noncalcium stone, nonoyster shell, dredged shell, and engineered reefs; (2) oyster restoration with alternative substrates occurs worldwide, but evaluations of alternative substrates were primarily (79%) within the United States of America; and (3) four main categories of performance metrics are used to assess alternative substrates—biological, structural, chemical, and economic acceptability. Within the four performance metrics, however, there exists a substantial variety in terms of specific metrics used and application of metrics to assess alternative substrates. Results highlight the need for common metrics across projects to ease comparison between alternative substrate options.

Quantifying Intertidal Habitat Relative Coverage in a Florida Estuary Using UAS Imagery and GEOBIA

Intertidal habitats like oyster reefs and salt marshes provide vital ecosystem services including shoreline erosion control, habitat provision, and water filtration. However, these systems face significant global change as a result of a combination of anthropogenic stressors like coastal development and environmental stressors such as sea-level rise and disease. Traditional intertidal habitat monitoring techniques are cost and time-intensive, thus limiting how frequently resources are mapped in a way that is often insufficient to make informed management decisions. Unoccupied aircraft systems (UASs) have demonstrated the potential to mitigate these costs as they provide a platform to rapidly, safely, and inexpensively collect data in coastal areas. In this study, a UAS was used to survey intertidal habitats along the Gulf of Mexico coastline in Florida, USA. The structure from motion photogrammetry techniques were used to generate an orthomosaic and a digital surface model from the UAS imagery. These products were used in a geographic object-based image analysis (GEOBIA) workflow to classify mudflat, salt marsh, and oyster reef habitats. GEOBIA allows for a more informed classification than traditional techniques by providing textural and geometric context to habitat covers. We developed a ruleset to allow for a repeatable workflow, further decreasing the temporal cost of monitoring. The classification produced an overall accuracy of 79% in classifying habitats in a coastal environment with little spectral and textural separability, indicating that GEOBIA can differentiate intertidal habitats. This method allows for effective monitoring that can inform management and restoration efforts.

Remote sensing of live and dead intertidal oyster reefs using aerial photo interpretation in Northeast Florida

The eastern oyster, Crassostrea virginica, has been classified as a keystone species as well as an ecosystem engineer because of the significant benefits that oysters and oyster reefs provide. Oyster reefs are being recognized as valuable for shoreline protection within coastal areas. The severe loss of oyster reef coverage has encouraged different types of conservation, mapping, monitoring and restoration efforts throughout its native range. Intertidal oyster reefs are an important habitat as well as an important industry in Florida, which makes accurate habitat monitoring a key element of resource management for this species. This project focused on creating a continuous intertidal oyster reef habitat map in northeast Florida. Existing aerial photography was used to identify oyster reef signatures, and map the distribution of intertidal oyster reefs throughout the study region using ArcGIS software. When accuracy assessment was completed, we found the number of observed agreements was 97% of the total observations. This mapping effort represents the first successful attempt at fine-scale oyster reef mapping across the entire northeast Florida region and resulted in a total of 17,953 individual reefs being mapped, with a total reef coverage of 651.86 ha. By using existing aerial photography, this methodology represents a low-cost method for reef mapping, compared to other methods such as drone imagery or field-based mapping. This baseline map of current oyster distribution will serve many functions for management this particular ecosystem. Future changes to reef distribution can be mapped and used to identify potential negative or positive impacts to the habitat.

A preliminary study on spatial assessment using conservation metrics for intertidal oyster reefs at the Hab River mouth in Pakistan

The oyster reefs in Pakistan are on the verge of extinction as a consequence of environmental and anthropogenic factors. A qualitative survey of oyster reef habitat was conducted from March-2017 to February-2018 in the Hab River Delta along the Balochistan coast (Arabian Sea), Pakistan. A combination of field survey and Geographical Information System (GIS) based approach (reef categorization, universal metrics and habitat suitability analysis), universal environmental variables, restoration goal-based metrics, sounding, condition indices, grain size composition and oyster spat-fall were determined for planning future oyster reef restoration efforts. The reefs were categorized into three main groups as dispersed, patch and continuous on the basis of fragmented spatial geometry. Dispersed reefs were more numerous than continuous and patch categories. The differences between morphometric measurements and density of oysters amongst reefs types were statistically insignificant. Habitat suitability analysis was done by ‘Benthic Terrain Modeler’ using ArcGIS software. The moderate, positive values of Bathymetric Position Index (BPI) of the oyster reef indicate an area of high or open slope with sea bottom (-2 to 6). The area of reef location shows high to moderate values of rugosity (0.7 to 0.9), indicates good to intermediate conditions; whereas, the aspect analysis showed slope orientation in the Northeast direction but mostly flat area. The environmental and restoration goal-based metrics were favorable for oyster growth and survival. The dispersed reefs showed lowest bathymetry points compared to patch and continuous reefs. The values of condition indices reveal not significant difference among reef types (continuous, dispersed and patch). Fine sand has the highest percentage (71%) followed by silt/clay fraction (18%). The higher density and spat size were recorded in monsoon (June to September) season. The current study suggests that the present reefs are viable and have potential for successful restoration and may be converted into a sizeable ecologic sanctuary.

Rapid and Accurate Monitoring of Intertidal Oyster Reef Habitat Using Unoccupied Aircraft Systems and Structure from Motion

Oysters support an economically important fishery in many locations in the United States and provide benefits to the surrounding environment by filtering water, providing habitat for fish, and stabilizing shorelines. Changes in oyster reef health reflect variations in factors such as recreational and commercial harvests, predation, disease, storms, and broader anthropogenic influences, such as climate change. Consistent measurements of reef area and morphology can help effectively monitor oyster habitat across locations. However, traditional approaches to acquiring these data are time-consuming and can be costly. Unoccupied aircraft systems (UAS) present a rapid and reliable method for assessing oyster habitat that may overcome these limitations, although little information on the accuracy of platforms and processing techniques is available. In the present study, oyster reefs ranging in size from 30 m2 to 300 m2 were surveyed using both fixed-wing and multirotor UAS and compared with ground-based surveys of each reef conducted with a real-time kinematic global positioning system (RTK-GPS). Survey images from UAS were processed using structure from motion (SfM) stereo photogrammetry techniques, with and without the use of ground control point (GCP) correction, to create reef-scale measures of area and morphology for comparison to ground-based measures. UAS-based estimates of both reef area and morphology were consistently lower than ground-based estimates, and the results of matched pairs analyses revealed that differences in reef area did not vary significantly by aircraft or the use of GCPs. However, the use of GCPs increased the accuracy of UAS-based reef morphology measurements, particularly in areas with the presence of water and/or homogeneous spectral characteristics. Our results indicate that both fixed-wing and multirotor UAS can be used to accurately monitor intertidal oyster reefs over time and that proper ground control techniques will improve measurements of reef morphology. These non-destructive methods help modernize oyster habitat monitoring by providing useful and accurate knowledge about the structure and health of oyster reefs ecosystems.