Water column structure influences variability of micronekton distribution and biodiversity in the California Current

• No trend in mixed layer depth (MLD) was found in the 34-year time series. • A shallower MLD was associated with higher relative abundance for 4 species. • Species richness decreased with an increase (deepening) in MLD. • 11 species displayed positive relationships with trawl depth and 6 were negative. Vertical water column characteristics are important features for understanding pelagic species’ distribution patterns, although they are rarely included as covariates in model-based abundance indices derived from fisheries-independent surveys. The mixed layer depth (MLD) is one such metric of the physical water column structure that could improve model-based estimates of abundance. In eastern boundary upwelling systems, water column stratification alters abiotic parameters, including temperature and availability of nutrients and light, above and below the MLD, potentially impacting the distribution and concentration of zooplankton and micronekton. To evaluate the role of MLD on individual species abundance and community biodiversity metrics, we examined 34 years (1990–2023) of catch and hydrographic data from a fisheries-independent midwater trawl survey of the epipelagic micronekton in the California Current. While global ocean models project a shoaling of the MLD with long-term ocean warming, we found no trend in MLD through time in our study area. However, we did find significant relationships between the abundance, or presence, of several species (krill, young-of-the-year [YOY] northern anchovy, YOY Pacific hake, adult Pacific sardine, YOY sanddabs, sergestid shrimp, and YOY widow rockfish), and overall species richness with MLD, which indicates that the catchability of some species may be influenced by the vertical water column structure. Additionally, we used auxiliary depth-stratified tows to assess vertical catch distributions and found significant relationships between trawl depth and species abundance and richness. Thus, accounting for MLD may reduce uncertainty in indices developed for both stock assessments and ecosystem status reports, as well as provide insights into the potential impacts of climate change on survey procedures.