San Francisco Estuary and Watershed Science

Abstract: Monitoring species abundance is a critical tool for identifying trends in wildlife populations. Using data collected in the San Francisco Bay Area between 1995 and 2019, we evaluated trends in nesting abundance of four Ardeid species across the entire study area and in 10 subregions, while accounting for the effect of rainfall. Overall, Great Egret (Ardea alba) nest abundance increased by 27% (95% confidence interval -1%, 54%) from 783 to 993 nests. Great Blue Heron (Ardea herodias) and Snowy Egret (Egretta thula) nesting abundance was similar across the study period, averaging approximately 503 and 509 nests, respectively, but Snowy Egret abundance was highly variable between years. Finally, Black-crowned Night-Heron (Nycticorax nycticorax) abundance declined -22% (95% confidence interval -59%, 15%) from 682 to 535 nests. At the subregional scale, trends were variable within species, and no species had consistent positive or negative trends across all 10 subregions, although it appears the distribution of all species except Great Blue Heron shifted among subregions. Our results suggest conservation action may be warranted to recover the Black-crowned Night-Heron population in our study area, but there is uncertainty on the magnitude and the reasons for their decline. Further investigation of the mechanisms for demographic change is needed to guide effective actions. In the absence of that mechanistic information, protection of the few colony sites occupied by Black-crowned Night-Herons and Snowy Egrets, especially islands in San Francisco Bay and two large urban colonies in Santa Rosa and Fairfield, is a prudent immediate action.

Effective waterfowl management relies on the collection of relevant demographic data to inform land-management decisions; however, some types of data are difficult to obtain. For waterfowl, brood surveys are difficult to conduct because wetland habitats often obscure ducklings from being visually assessed. Here, we used Unoccupied Aerial Systems (UAS) to assess what wetland habitat characteristics influenced brood abundance in Suisun Marsh, California, USA. Using a thermal-imaging camera, we surveyed 17 wetland units that encompassed 332ha of flooded area on the premises of seven waterfowl hunting clubs during the waterfowl breeding season. Additionally, using a combination of multi-spectral imagery collected from the UAS flights and LiDAR data from the previous year, we mapped habitat composition within each unit to relate to brood observation counts. From June 3–7, 2019, we identified 113 individual broods comprising 827 ducklings. We found a positive relationship between the number of broods observed and the proportion of the unit that was flooded. We also found a positive relationship between the number of broods observed and the area of effective habitat—a metric of flooded habitat within two times the 95th-percentile Euclidean distance that all broods were observed from any vegetated cover. Brood surveys using UAS could complement the traditional Breeding Population Survey and provide local managers with fine-scale and timely information about shifts in brood abundance in the region.

Flooding rice (Oryza sativa) agricultural fields during winter to facilitate rice straw decomposition has mitigated the loss of some of the natural wetlands in California’s Central Valley. We conducted bird surveys in 253 rice checks (2,158 ha) within 177 rice fields in the Sacramento Valley during the fall and winter of 2021–2022 and 2022–2023 to evaluate factors that influence bird use of winter-flooded, post-harvest rice fields enrolled in the California Winter Rice Habitat Incentive Program. We counted 143,932 birds from 57 species, including dabbling ducks (86.4%), geese (8.0%), shorebirds (0.9%), wading birds (0.7%), and other birds (4.0%). Extrapolating from the lowest densities observed in rice fields during the 70-day mandatory flooding period, we estimated that properties enrolled in this public–private partnership provided habitat for at least 271,312 birds day-1 (16,248 ha; 2021–2022) and 147,315 birds day-1 (8,448 ha; 2022–2023), totaling >10 million bird-use-days each winter. Water depth had the greatest influence on bird abundance and diversity. Relatively shallow water depths (≤13 cm) had greater abundance of shorebirds, wading birds, and geese, and higher diversity, whereas intermediate depths (~23 cm) resulted in the greatest dabbling duck abundance. Duck, goose, and wading bird abundances were greatest—and species richness and family diversity were highest—8 days after the onset of flooding in rice fields (typically late October), followed by a decline in bird use until 65 to 87 days post-flooding, after which bird use increased slightly. Bird abundance and species diversity were lowest in rice fields with the greatest hunting intensity (≥3 days week-1). We identified several habitat variables that could be managed and prioritized by land-owner incentive programs to increase bird use of winter-flooded rice, including water depth, variation in emergent vegetation height, mudflat habitat availability, rice check shape, hunting intensity, and post-harvest treatment of residual rice straw.

Striped Bass (Morone saxatilis) monitoring and research in California’s Central Valley primarily occurs in the Sacramento River basin and the Sacramento–San Joaquin Delta. A relatively under-studied contingent of the Striped Bass population is present in the San Joaquin River and its tributaries. One such tributary, the Stanislaus River, is an important source of natural production of native anadromous fishes, including fall-run Chinook Salmon (Oncorhynchus tshawytscha), Steelhead (O. mykiss), and Pacific Lamprey (Entosphenus tridentatus). Because Striped Bass are a non-native piscivore, characterizing when and where their distribution overlaps with native fishes is a first step to assessing the potential for negative inter-specific interactions. We compiled incidental observations of Striped Bass made during long-term (1996 to 2021) salmonid monitoring programs performed at different times of the year, and found that Striped Bass were present at monitoring locations throughout most of the year, although not detected in every year. We also used data on Striped Bass captured during boat electro-fishing surveys conducted during the 2019, 2020, and 2021 juvenile salmonid emigration season (February to June), for a more detailed evaluation of Striped Bass occupancy within the lower 65 kilometers of the Stanislaus River. Median fork length (FL) of Striped Bass captured from February to April was significantly larger than those captured in May and June (p < 0.001). Using dynamic occupancy models, we showed that Striped Bass larger than 300 mm FL were present, and their occupancy increases earlier in the year than individuals under 300 mm FL. In all 3 years, occupancy estimates were greater than 80% of the lower Stanislaus River by May. Our results suggest a high degree of spatial and temporal overlap with native migratory fishes, which may have important implications for understanding and managing how predation affects juvenile salmon and other native species.