Estuarine-terrestrial habitat gradients enhance nursery function for resident and transient fishes in the San Francisco Estuary

Nursery functions of US West Coast drowned river valley estuaries are not well understood. Using long-term fish-monitoring data (1995-2017) in Suisun Marsh, San Francisco Estuary, California, USA, we examined spatial and temporal trends in abundance and apparent growth of fishes with diverse life-history types. Focal species were Sacramento splittail Pogon-ichthys macrolepidotus, striped bass Morone saxatilis, tule perch Hysterocarpus traski, and starry flounder Platichthys stellatus, which collectively represented 55% of total catch (n = 140 092). We identified keystone habitat patches that functioned as nursery hotspots during the peak young-of-the-year recruitment window. Deep, flow-through sloughs close to the open estuary were important nursery habitats for the marine transient starry flounder. In contrast, splittail and striped bass mostly migrated through such corridors to rear in shallow, dead-end sloughs transecting tidal marsh plains, managed tidal ponds, and uplands. Tule perch were concentrated in shallow, interior sloughs, reflecting their resident life-history type and adaptations to variable conditions in a small home range. Interactions among freshwater flows and stationary habitat features (e.g. channel depth, land-to-open-water ratio) were related to fish abundance; however, species and age classes differed in their relationships to these interactions, suggesting a mechanism for habitat partitioning in space and time. Overall, we inferred that habitat connectivity - longitudinal, lateral, and vertical - along the estuarine-terrestrial gradient was a driver of fish species diversity and productivity. Consideration of seascape-landscape dynamics across multiple spatial and temporal scales in estuaries should help maintain or increase fish populations and ecological resilience in the face of rising sea levels and other environmental stressors