Haul-out Research Articles

Enhancing the accuracy and efficiency of Pacific walrus (Odobenus rosmarus divergens) surveys: A comparison of visual and aerial imagery-based counts at coastal haulouts.

This study presents a semi-automated approach utilizing unoccupied aerial vehicle (UAV) surveys to accurately estimate the abundance of Pacific walruses at large coastal haulouts in Chukotka, Russia. Seven major haulout sites were surveyed during the summers and falls of 2017-2019. Walrus counts were performed using three distinct methods: traditional visual land-based counts, complete head counts utilizing georeferenced UAV imagery, and counting walruses within model polygons within the haulout outline and employing various extrapolation techniques to predict walrus abundance across the haulout area. The results indicated that traditional visual counts neither yielded consistent results nor allowed for uncertainty estimation, unlike the site- and date-specific direct extrapolation method and the non-specific linear regression model. These latter methods consistently provided estimates, on average, within 5% of the "true" abundance determined through complete photo-based head counts. Beside yielding accurate estimates, these semi-automated methods significantly reduced counting time by at least 63%, in contrast to complete head counts. The non-specific model, which allowed the estimation of walrus abundance based on the type of the terrain and the haulout area was less accurate compared with site and date specific estimates, but provided a tool to estimate abundance when no field visits are conducted, e.g., by using high-resolution satellite imagery to measure haulout area. This model revealed that the haulouts located on flat sandy beaches exhibited mean walrus densities approximately 30.5% times higher than those on rocky shores surrounded by cliffs: 0.879 (SD = 0.1302) and 0.648 (SD = 0.1753) walrus per m2 correspondingly. The estimated daily walrus abundance at major Chukotkan haulouts in 2017-2019 ranged between 15 and 94,660 (mean = 10,397, SD = 14,477) walruses with the maximum seasonal abundances reported at Cape Serdtse-Kamen as 94,960 on 10-Oct-2017, 26,850 on 10-Oct-2018, and 87,595 on 10-Oct-2019.

Sex-specific diet differences in harbor seals (Phoca vitulina) via spatial assortment.

The lack of recovery of Chinook salmon (Oncorhynchus tshawytscha) in the Pacific Northwest has been blamed in part on predation by pinnipeds, particularly the harbor seal (Phoca vitulina). Previous work at a limited number of locations has shown that male seal diet contains more salmon than that of female seals and that sex ratios at haul-out sites differ spatiotemporally. This intrapopulation variation in predation may result in greater effects on salmon than suggested by models assuming equal spatial distribution and diet proportion. To address the generality of these patterns, we examined the sex ratios and diet of male and female harbor seals from 13 haul-out sites in the inland waters of Washington State and the province of British Columbia during 2012-2018. DNA metabarcoding was conducted to determine prey species proportions of individual scat samples. The sex of harbor seals was then determined from each scat matrix sample with the use of quantitative polymerase chain reaction (qPCR). We analyzed 2405 harbor seal scat samples using generalized linear mixed models (GLMMs) to examine the factors influencing harbor seal sex ratio at haul-out sites and permutational multivariate analysis of variance (PERMANOVA) to examine the influence of sex and haul-out site on harbor seal diet composition. We found that the overall sex ratio was 1:1.02 (female:male) with notable spatiotemporal variation. Salmoniformes were about 2.6 times more abundant in the diet of males than in the diet of females, and Chinook salmon comprised ca. three times more of the average male harbor seal's diet than the average female's diet. Based on site-specific sex ratios and diet data, we identified three haul-out sites where Chinook salmon appear to be under high predation pressure by male harbor seals: Cowichan Bay, Cutts Area, and Fraser River. Our study indicates that combining sex-specific pinniped diet data with the sex ratio of haul-out sites can help identify priority sites of conservation concern.

Feeding of the caspian seal (Pusa caspica Gmelin, 1788) during haul out periods at the Kenderli rookery (Middle Caspian)

The Kendirli Haul-Out Site of the Caspian Seal served as the sole haul-out location in the Central Caspian Sea. Consequently, data obtained regarding the seal's diet at this site holds significant importance for the study and conservation of the Caspian Seal population. This study analyzed the diet of the Caspian Seal based on fecal collections from the Kendirli Haul-Out Site spanning from 2015 to 2019. Given the Caspian Seal's endangered status, a vital in vivo method of coprological analysis was employed to assess its diet. Comparative analysis of the seal's diet was conducted across seasons and years, and fish lengths consumed by seals were determined using otoliths extracted from feces. The study revealed that the Caspian Seal's diet at the Kendirli Haul-Out Site comprises 11 fish species, including species of the Cyprinidae family and Benthophilus genus, along with unidentified species of gobies. It was observed that the seal's diet varies seasonally; during autumn, the primary food source consists of gobies, whereas in spring, Atherina caspia predominates the diet. Additionally, carp species, Clupeonella caspia, and Alosa braschnikowi are present in the spring diet but absent in the autumn diet. Reconstruction of fish length ranges for three fish species — Neogobius melanostomus affinis, N. pallasi, and Alosa braschnikowi — demonstrated that seals consume fish ranging from 30 to 260 mm in length.

Estimating the risks of exposure to harmful algal toxins among Scottish harbour seals

Harmful algal bloom (HAB) toxins consumed by marine predators through fish prey can be lethal but studies on the resulting population consequences are lacking. Over the past approximately 20 years there have been large regional declines in some harbour seal populations around Scotland. Analyses of excreta (faeces and urine from live and dead seals and faecal samples from seal haulout sites) suggest widespread exposure to toxins through the ingestion of contaminated prey. A risk assessment model, incorporating concentrations of the two major HAB toxins found in seal prey around Scotland (domoic acid (DA), and saxitoxins (STX)), the seasonal persistence of the toxins in the fish and the foraging patterns of harbour seals were used to estimate the proportion of adults and juveniles likely to have ingested doses above various estimated toxicity thresholds. The results were highly dependent on toxin type, persistence, and foraging regime as well as age class, all of which affected the proportion of exposed animals exceeding toxicity thresholds. In this preliminary model STX exposure was unlikely to result in mortalities. Modelled DA exposure resulted in doses above an estimated lethal threshold of 1900 µg/kg body mass affecting up to 3.8 % of exposed juveniles and 5.3 % of exposed adults. Given the uncertainty in the model parameters and the limitations of the data these conclusions should be treated with caution, but they indicate that DA remains a potential factor involved in the regional declines of harbour seals. Similar risks may be experienced by other top predators, including small cetaceans and seabirds that feed on similar prey in Scottish waters.

Human Impact on the Twenty-Four-Hour Patterns of Steller Sea Lions' Use of a Haulout in Hokkaido, Japan.

Steller sea lions (SSLs) migrate to the Hokkaido coast to spend the winter there, leading to conflicts arising with fishermen over herring. This study analyzed the trends in the SSLs' use of a haulout as a rest site under human pressure. From January to March in 2017, 2018, and 2019, we recorded the SSL behavior at the haulout site off Otaru City, Hokkaido, for 24 h a day using a fixed-point video recorder. We investigated three years of data to analyze the relationships between the SSL behaviors (attendance/landing-entry timings/remaining on land) and herring caught. We also monitored the SSL behaviors during changes in weather conditions and under human pressure. Throughout the three years, the SSLs used the haulout site during harsher weather or under human pressure. In 2017 and 2018, there was a correlation between the herring caught and the maximum number of SSLs on the haulout, but not in 2019. The number of SSLs on the haulout increased from evening to night; most individuals entered the water in the morning. The SSLs probably return to the water around sunrise not only for foraging but also to avoid anthropogenic pressure. The damage caused to the herring fishery by the SSLs was severe, but it is also clear that human pressure changed their behavior in response.

Haulout Patterns of Harbour Seal Colonies in the Norwegian Skagerrak, as Monitored through Time-Lapse Camera Surveys

Harbour seals (Phoca vitulina) are part of the Norwegian coastal ecosystem and can be observed on skerries, islands, and sandbanks along the coastline, sometimes in close proximity to inhabited areas. In this study, we used time-lapse camera surveys to monitor the haulout patterns of harbour seals at two selected sites in the Norwegian Skagerrak, Lyngør and Østre Bolæren, over 12 and 4 months, respectively. The goal was to investigate how the number of seals hauling out on land varied seasonally and how it was influenced by environmental parameters (wind speed, air temperature, and water level), the time of the day, and anthropogenic disturbances. As expected, the number of seals hauled out increased with increasing air temperature and decreased with increasing wind speed and water level. Clear circadian patterns in the seal haulout behaviour were identified during autumn and winter when a significantly higher number of seals were observed on land at night. Moreover, haulout patterns showed significant seasonal variation, with a peak in haul outs being observed during the moulting season in August. Despite an expected high usage of land during the breeding season in early summer, the number of seals hauled out at the Lyngor study site was low during this period, especially during weekends and summer holidays, maybe due to increased disturbance from boats. This study provides valuable insights into the factors influencing the haulout behaviour of the species in the region and suggests possible effects of human disturbance on harbour seal behaviour in the area.

Validation of satellite imagery for quantitative population assessment and monitoring of Atlantic walrus

Monitoring animal population abundance and distribution is essential for conservation and management. Recent advances in very high-resolution (VHR) satellite imagery allow for unprecedented detection and identification of animals, offering a potential alternative to conventional methods of population assessment such as aerial surveys. Here, we compare satellite and aerial survey images of a terrestrial walrus haul-out site in the Canadian High Arctic taken 1.5 h apart. While the 30-cm resolution of the commercially available satellite image was insufficient to reliably count individual walruses visually, a manual digitization method successfully identified and delineated image areas confirmed visually to have walrus. Estimates of numbers of hauled out walrus obtained by multiplying the detected area by a range of densities in the aerial image (231) agreed well with actual counts in 35 and 55 mm aerial images (217–240). Potential applications of this approach include quantitative abundance estimation or more simple monitoring of presence/absence over large expanses of remote areas that are logistically difficult to cover using survey aircraft.

Ontogeny of movement patterns in naïve grey seal pups inhabiting a complex continental shelf ecosystem.

Most vertebrate offspring must transition from the relative security of parental care (nutrition and protection) to independent foraging. Offspring face many challenges during this critical period, particularly in species where parental care ends at weaning, such as the grey seal (Halichoerus grypus). We studied the development of movement behaviour in naïve grey seal pups from their first trips to sea to about five months of age. Twenty-five (12 males and 13 females) newly-weaned pups were fitted with satellite-linked GPS tags on Sable Island, Nova Scotia, Canada in January 2016. The influence of fixed effects (pup size, sex, week) and the random effect of pup identity on trip characteristics were examined. Movement behaviour was analyzed using a move persistence mixed-effects model. Habitat use was highly variable among individuals and covered much of the geographic distribution of the population. Unlike older juveniles, subadults, and adults in this population, most naïve pups used multiple haulout sites to begin and end trips. There was little evidence of area-restricted search behaviour during trips, suggesting that naïve pups were using an opportunistic foraging tactic that may result in more variable foraging success than that of older, experienced animals. Naïve pups made longer trips with longer haulout durations between them than observed for older greys seals. Males and females differed in some trip characteristics, but sex effects were small over the first few months of life. Offspring size at weaning was not a useful predictor of trip characteristics. Move persistence of grey seal pups was initially high and then decreased over time as individuals gained experience. Both intrinsic and extrinsic factors were influential on the movements of grey seal pups. Greater body length at weaning, longer duration spent on shore after weaning, shallower water column depth, and farther distance from shore were all associated with lower move persistence. Female grey seal pups had lower move persistence than males. Overall, the movements of naïve grey seal pups during the first few months of life were characterized by extensive exploration, but move persistence decreased over time suggesting they may be using an exploration-refinement foraging tactic.

Correction: Haul-out site use by Ladoga ringed seal (Pusa hispida ladogensis) on the islands of the Valaam Archipelago

Correction: Haul-out site use by Ladoga ringed seal (Pusa hispida ladogensis) on the islands of the Valaam Archipelago

Habitat selection of southern giant petrels: potential environmental monitors of the Antarctic Peninsula

AbstractThe southern giant petrel (Macronectes giganteus) is a widely distributed top predator of the Southern Ocean. To define the fine-scale foraging areas and habitat use of Antarctic breeding populations, 47 southern giant petrels from Nelson Island were GPS-tracked during the summers of 2019–2020 and 2021–2022. Step-selection analysis was applied to test the effects of environmental variables on habitat selection. Visual overlap with seal haul-out sites and fishing areas was also analysed. Birds primarily used waters to the south of the colony in the Weddell and Bellingshausen seas. Females showed a broader distribution, reaching up to -70°S to the west of Nelson Island, while males were mainly concentrated in waters off the northern Antarctic Peninsula. Habitat selection of both sexes was associated with water depth and proximity to penguin colonies. Both overlapped their foraging areas with fishing sites and females in particular overlapped with toothfish fishery blocks in Antarctica and with fishing areas in the Patagonian Shelf. Due to their habitat associations and overlap with fisheries, when harnessed with tracking devices and animal-borne cameras, giant petrels can act as platforms for monitoring the condition and occurrence of penguin colonies, haul-out sites and unregulated fisheries on various temporal and spatial scales in Antarctica.

Haul-out patterns of the Baltic grey seal (Halichoerus grypus) in the suburbs of a metropolis

In this study, we investigated the haul-out patterns of the Baltic grey seal in the coastal area adjacent to the metropolitan city, Saint Petersburg, during the ice-free seasons of 2017-2022. Grey seals occupied stony banks near Kotlin Island, in the easternmost part of the Gulf of Finland. The censuses were carried out from the island shore during evening hours. The number of seals reached 70 during the survey. Contrary to the common trend reported in similar studies, the annual minimum in seal abundance (May and June) coincided with the peak of moulting. Active use of the haul-out site was observed between July and November, implying that eastward movements of the grey seals take place in the Gulf of Finland in the post-moulting period. Wind speed and sea state interfered with the seal hauling out throughout the year, whereas the relationship with air temperature varied seasonally. Cloud cover, atmospheric pressure, wind direction and sea level had no impact on the seal number, though the fluctuations in sea level reduced the haul-out space. The tendency of the seals to haul out towards and after the sunset was determined. The most frequent sources of human disturbance were light planes (0.45 ± 0.12 confidence interval, per count) and powerboats (0.41 ± 0.14 confidence interval, per count), but only the powerboats significantly decreased the seal number. We found that the seals used the banks concurrently with seabirds. The area of Kotlin Island presumably attracts the seals by the diversity of prey items in the estuary of the Neva River. Establishing of a marine protected area and physical marking of the water space around the haul-out site are recommended.

Haul-out site use by Ladoga ringed seal (Pusa hispida ladogensis) on the islands of the Valaam Archipelago

Haul-out site use by Ladoga ringed seal (Pusa hispida ladogensis) on the islands of the Valaam Archipelago

Effects of anthropogenic noise on haul-out numbers of harbor seals (Phoca vitulina)

Haul-out sites of harbor seals, Phoca vitulina Linnaeus, 1758, include areas with high levels of anthropogenic noise. In some cases, seals haul out at night when there are lower in-air noise levels. However, it is unclear whether there are additional responses to noise pollution. To determine potential impacts of anthropogenic noise on haul-out behavior, we compared numbers of hauled-out harbor seals relative to in-air noise levels at two sites in Washington state, USA—one close to human activities (Bellingham waterfront) and one more distant (Semiahmoo marina)—between July 2020 and August 2021. We used generalized linear mixed models to identify predictors of seal numbers. The marina had lower mean noise levels than the waterfront (39.7 ± SD 6.1 dB, n = 29 observations versus 51.2 ± SD 5.2 dB, n = 126 observations). The plotted model prediction showed a significantly negative association between noise and seals at the marina, and no association was found at the waterfront. Results indicate that in-air noise levels may influence seal numbers at sites where human activities are low. They also suggest that, besides hauling out at night, seals may become tolerant to in-air noise levels at sites where human activities are high.

New data on South American fur seals and sea lions' occupation of the Wildlife Refuge of Ilha dos Lobos, southern Brazil

Abstract We present the most recent data on the seasonal and spatial occupation of South American sea lions (Otaria flavescens) and fur seals (Arctocephalus australis) in the Wildlife Refuge of Ilha dos Lobos (WRIL) in southern Brazil throughout the year, based on aerial photographic counts. Thirty-one aerial photographic counts were conducted between July 2019 and November 2020 to assess monthly differences in the abundance of pinnipeds in the WRIL. The results were analysed using a generalized linear model. Spatial analysis was performed using kernel density. Subadult males of South American sea lion were the most abundant pinniped in the WRIL, followed by juveniles of South American fur seal. A juvenile of Southern elephant seal (Mirounga leonina) was also recorded. South American fur seals showed a marked seasonality, occurring only between July and October, while South American sea lions occurred year-round. Among the months analysed, September exhibited the highest mean abundance (mean 113.75; SD: ± 8.58), followed by August (mean 103.00; SD: ± 15.69). The pinnipeds were more often concentrated in the northern and central parts of the island. This study reinforces the importance of the WRIL as a haulout site for pinnipeds. Considering the seasonal occupation of the island by South American pinnipeds, monitoring is recommended prior to the development of activities in the area.

Brown bear–sea otter interactions along the Katmai coast: terrestrial and nearshore communities linked by predation

AbstractSea otters were extirpated throughout much of their range by the maritime fur trade in the 18th and 19th centuries, including the coast of Katmai National Park and Preserve in southcentral Alaska. Brown bears are an important component of the Katmai ecosystem where they are the focus of a thriving ecotourism bear-viewing industry as they forage in sedge meadows and dig clams in the extensive tidal flats that exist there. Sea otters began reoccupying Katmai in the 1970s where their use of intertidal clam resources overlapped that of brown bears. By 2008, the Katmai sea otter population had grown to an estimated 7,000 animals and was likely near carrying capacity; however, in 2006–2015, the age-at-death distribution (AADD) of sea otter carcasses collected at Katmai included a higher-than-expected proportion of prime-age animals compared to most other sea otter populations in Alaska. The unusual AADD warranted scientific investigation, particularly because the Katmai population is part of the Threatened southwest sea otter stock. Brown bears in Katmai are known to prey on marine mammals and sea otters, but depredation rates are unknown; thus, we investigated carnivore predation, especially by brown bears, as a potential explanation for abnormally high prime-age otter mortality. We installed camera traps at two island-based marine mammal haulout sites within Katmai to gather direct evidence that brown bears prey on seals and sea otters. Over a period of two summers, we gathered photo evidence of brown bears making 22 attempts to prey on sea otters of which nine (41%) were successful and 12 attempts to prey on harbor seals of which one (8%) was successful. We also developed a population model based on the AADD to determine if the living population is declining, as suggested by the high proportion of prime-age animals in the AADD. We found that the population trend predicted by the modeled AADDs was contradictory to aerial population surveys that indicated the population was not in steep decline but was consistent with otter predation. Future work should focus on the direct and indirect effects these top-level predators have on each other and the coastal community that connects them.

Forecasting shifts in habitat suitability of three marine predators suggests a rapid decline in inter-specific overlap under future climate change.

Understanding how environmental and climate change can alter habitat overlap of marine predators has great value for the management and conservation of marine ecosystems. Here, we estimated spatiotemporal changes in habitat suitability and inter‐specific overlap among three marine predators: Baltic gray seals (Halichoerus grypus), harbor seals (Phoca vitulina), and harbor porpoises (Phocoena phocoena) under contemporary and future conditions. Location data (>200 tagged individuals) were collected in the southwestern region of the Baltic Sea; one of the fastest‐warming semi‐enclosed seas in the world. We used the maximum entropy (MaxEnt) algorithm to estimate changes in total area size and overlap of species‐specific habitat suitability between 1997–2020 and 2091–2100. Predictor variables included environmental and climate‐sensitive oceanographic conditions in the area. Sea‐level rise, sea surface temperature, and salinity data were taken from representative concentration pathways [RCPs] scenarios 6.0 and 8.5 to forecast potential climate change effects. Model output suggested that habitat suitability of Baltic gray seals will decline over space and time, driven by changes in sea surface salinity and a loss of currently available haulout sites following sea‐level rise in the future. A similar, although weaker, effect was observed for harbor seals, while suitability of habitat for harbor porpoises was predicted to increase slightly over space and time. Inter‐specific overlap in highly suitable habitats was also predicted to increase slightly under RCP scenario 6.0 when compared to contemporary conditions, but to disappear under RCP scenario 8.5. Our study suggests that marine predators in the southwestern Baltic Sea may respond differently to future climatic conditions, leading to divergent shifts in habitat suitability that are likely to decrease inter‐specific overlap over time and space. We conclude that climate change can lead to a marked redistribution of area use by marine predators in the region, which may influence local food‐web dynamics and ecosystem functioning.

SEALNET: Facial recognition software for ecological studies of harbor seals.

Methods for long‐term monitoring of coastal species such as harbor seals (Phoca vitulina) are often costly, time‐consuming, and highly invasive, underscoring the need for improved techniques for data collection and analysis. Here, we propose the use of automated facial recognition technology for identification of individual seals and demonstrate its utility in ecological and population studies. We created a software package, SealNet, that automates photo identification of seals, using a graphical user interface (GUI) software to detect, align, and chip seal faces from photographs and a deep convolutional neural network (CNN) suitable for small datasets (e.g., 100 seals with five photos per seal) to classify individual seals. We piloted the SealNet technology with a population of harbor seals located within Casco Bay on the coast of Maine, USA. Across two years of sampling, 2019 and 2020, at seven haul‐out sites in Middle Bay, we obtained a dataset optimized for the development and testing of SealNet. We processed 1752 images representing 408 individual seals and achieved 88% Rank‐1 and 96% Rank‐5 accuracy in closed set seal identification. In identifying individual seals, SealNet software outperformed a similar face recognition method, PrimNet, developed for primates but retrained on seals. The ease and wealth of image data that can be processed using SealNet software contributes a vital tool for ecological and behavioral studies of marine mammals in the developing field of conservation technology.

Extreme moulting site fidelity of the Saimaa ringed seal

Site fidelity is commonly observed in pinnipeds and has direct consequences for individual space use and population dynamics. Here, we used photo-identification recapture data to quantify site fidelity of the endangered Saimaa ringed seal (Pusa hispida saimensis) over four successive moulting seasons. We identified 337 seals based on their permanent fur patterns, and 192 of them were observed during at least 2 years. Over the study period, the median number of terrestrial haul-out sites used by an individual seal was four, and nearly 50% of the seals reused them over the years. Although eight seals performed movements (up to 48 km) between the different water basins of Lake Saimaa, most of the studied seals remained in the same water basin over the years. The median distance between successive moulting sites used by an individual seal was 643 m. While these distances were similar within years in both sexes, the distances between years were longer in females, suggesting post-nursing related behaviour. The extreme site fidelity of the Saimaa ringed seal has important implications for its conservation, especially in the land use management of the Lake Saimaa shoreline.

Exposure of individual harbour seals (Phoca vitulina) and waters surrounding protected habitats to acoustic deterrent noise from aquaculture

Abstract Pinniped depredation at aquaculture sites is a globally recognized problem. To mitigate depredation, the aquaculture sector uses acoustic deterrent devices (ADDs) as a non‐lethal alternative to shooting pinnipeds interacting with caged finfish. However, it is unclear whether sound emissions from ADDs have the potential to also impact non‐target pinnipeds at spatial scales relevant to populations. Global Positioning System (GPS) tracking data from seven harbour seals tagged in a non‐aquaculture context, on the west coast of Scotland, in 2017 were combined with modelled maps of ADD noise to quantify sound exposure and estimate the potential for auditory impairment. The acoustic model applied an energy flux approach across the main frequency range of ADDs (2–40 kHz). Predictions of temporary and permanent auditory threshold shifts were made using seal location data and published noise exposure criteria. The acoustic exposure of waters (10‐km buffers) surrounding protected habitats (i.e. designated haul outs and Special Areas of Conservation (SACs)) on the west coast of Scotland was also assessed. All tagged seals and waters surrounding 51 of 56 protected sites were predicted to be exposed to ADD noise exceeding median ambient sound levels. Temporary auditory impairment was predicted to occur in one of the seven tagged harbour seals and across 1.7% of waters surrounding protected habitats over a 24‐hour period, when assuming a 100% ADD duty cycle. Although the predicted risk of auditory impairment appears to be relatively low, these findings suggest that harbour seals inhabiting inshore waters off western Scotland are routinely exposed to ADD noise that exceeds median ambient sound levels. This chronic exposure risks negative consequences for individual harbour seals among the wider population in this region. The use of ADDs to mitigate pinniped depredation should be carefully considered to reduce unintended habitat‐wide impacts on non‐target species, including pinnipeds that are not specifically interacting with aquaculture.

Data on the diets of Salish Sea harbour seals from DNA metabarcoding

Marine trophic ecology data are in high demand as natural resource agencies increasingly adopt ecosystem-based management strategies that account for complex species interactions. Harbour seal (Phoca vitulina) diet data are of particular interest because the species is an abundant predator in the northeast Pacific Ocean and Salish Sea ecosystem that consumes Pacific salmon (Oncorhynchus spp.). A multi-agency effort was therefore undertaken to produce harbour seal diet data on an ecosystem scale using, 1) a standardized set of scat collection and analysis methods, and 2) a newly developed DNA metabarcoding diet analysis technique designed to identify prey species and quantify their relative proportions in seal diets. The DNA-based dataset described herein contains records from 4,625 harbour seal scats representing 52 haulout sites, 7 years, 12 calendar months, and a total of 11,641 prey identifications. Prey morphological hard parts analyses were conducted alongside, resulting in corresponding hard parts data for 92% of the scat DNA samples. A custom-built prey DNA sequence database containing 201 species (192 fishes, 9 cephalopods) is also provided.