Data from: Spatiotemporal variability from physics to plankton ecology in an upwelling bay

Abstract Bays play a critical role in Eastern Boundary Upwelling Systems (EBUS) as hotspots of biological productivity and incubators for commercially important species. Within the California EBUS, Monterey Bay is a well-studied upwelling bay located downstream of the Año Nuevo upwelling center. Spatial structuring includes enhanced phytoplankton blooms in the northern and southern bay due to the influx of nutrient-rich upwelled water and locally enhanced residence time and stratification. Temporal structuring includes a clear seasonal succession in phytoplankton taxa, as first diatoms and then dinoflagellates bloom. These characteristics have been described from satellite data, fixed-point time series, and process studies. However, characterizing spatiotemporal patterns of variability within Monterey Bay, their relation to environmental forcing, and physical-biological coupling requires a long-term, multidisciplinary, spatially and vertically resolved time series. Here, we summarize monthly high-resolution autonomous underwater vehicle (AUV) transects from 2016 to 2024 that survey Monterey Bay from inner to outer shelf habitats. The AUV measures physical (temperature, salinity), chemical (oxygen, nitrate), and biological (fluorescence, bioluminescence) parameters, and provides qualitative ecological information on photosynthetic and heterotrophic plankton communities. Our results highlight the importance of upwelling in shaping the Monterey Bay ecosystem. Dominant variability for most parameters is found to be strongly seasonal and coherent across the bay, and to be correlated with upwelling and each other for physics, chemistry, and part of the plankton community (i.e. diatoms). Dinoflagellates and zooplankton display contrasting dynamics apparently unrelated to upwelling, likely associated with stratification (dinoflagellates) and the end of blooms (zooplankton). Dataset description This dataset includes 2 files: gridded AUV surveys, collected approximately monthly in a diamond pattern in Monterey Bay from 2016 to 2024, saved as a NetCDF file. Metadata is given in the NetCDF file. the corresponding gulper data used to evaluate plankton proxies, saved as a csv file where columns G-L are the 18S eDNA read counts summed by broad taxonomic groups, columns M-N are matching variables measured by autonomous sensors onboard the vehicle, and columns O-R are matching proxies computed from full-resolution bioluminescence and/or fluorescence data. Details regarding data sources and calculations can be found in Messié et al. (2026).