UC Davis

The San Francisco Estuary (Estuary) is a novel ecosystem consisting of a unique community of native and nonnative organisms and a mosaic of human-constructed and naturalistic waterways, wetlands, and landscapes. The Estuary is highly altered and managed to support California’s waterfowl hunting heritage and valuable agriculture industry and is considered one of the most invaded in the world, leading to declines of native and pelagic fishes. Most estuaries suffer from eutrophication and harmful algal blooms, but the modifications and introduced species of the estuary create a situation where phytoplankton is limited. Tidal restoration has become a primary tool to recover diminished ecosystem function and conserve native species. The North Delta Arc (Arc), an arc of habitat in the upper Estuary, contains more habitat heterogeneity, hosts a higher proportion of native species, and has a geomorphology that allows for adaptation to sea-level-rise. These attributes of the Arc make it a seemingly prime candidate for tidal restoration within the Estuary; however, outcomes of restoration are largely unknown and effects of human-managed wetlands and landscapes on aquatic ecosystems are poorly understood. To address these knowledge gaps, I studied different aspects of restoring wetlands, tidal sloughs that are influenced by human managed wetlands and landscapes, and the managed wetlands and landscapes themselves. Suisun Marsh lies within the brackish water portion of the Arc and is primarily managed by private landowners and state agencies for waterfowl production and hunting. A common assumption has been that wetlands managed for waterfowl hunting created more harm than benefit for native fish species, which led to legislation requiring that much of the managed wetlands be restored to tidal wetlands. The first tidal restoration in Suisun Marsh was completed in 2006 and fishes within the restoration went largely unmonitored. I designed a study to describe fish communities and metrics of primary and secondary production within the restoring wetland, adjacent tidal slough channels, and a wetland actively managed for waterfowl hunting. I found that the restoration supported mainly nonnative species and a lower fish diversity than surrounding tidal habitats and the managed wetland. I also found far higher concentrations of chlorophyll a and zooplankton in the managed than the restoring marsh. The Cache Slough Complex makes up a majority of the freshwater portion of the Arc, is surrounded by agricultural land, and has more phytoplankton, zooplankton, and pelagic and native fishes than other freshwater regions of the Estuary. To understand the contribution of upstream agriculture in providing pelagic productivity and habitat for native fishes, I designed two research projects within the Cache Slough Complex and its watersheds. The first project measured nutrients, phytoplankton, and rates of pelagic primary production and respiration across sites with varying areas of upstream cropland. My study indicates that upstream cropland is important for phytoplankton production within the Cache Slough Complex. I also sampled fishes and invertebrates within the agricultural canals and ditches in watersheds that connect to the Cache Slough Complex. I found assemblages of native and nonnative fishes in the agricultural waterways and an abundance of invertebrates to feed them. Sites in watersheds with more irrigated cropland and no barrier to upstream migration supported the highest number of species. Contrary to common belief, my studies indicate that there are beneficial aspects of the working lands to aquatic ecosystems in the Estuary. Instead of a pure focus on restoring estuarine habitats to some unattainable historic state, my research suggests that management of working lands should be harnessed to benefit aquatic communities. Working landscapes have infrastructure to easily manipulate hydroperiods and water flows, so future research should be focused on how to best use these tools to attain specific ecosystem functions and conservation goals.