Floodplain inundation and lateral connectivity promote productivity in a managed river ecosystem

River-floodplain ecosystems near urban centers are heavily engineered for flood protection and water delivery, which has led to a loss of lateral hydrologic connectivity between rivers and their floodplains. This study has two objectives: (1) Does increased lateral connectivity resulting from floodplain inundation increase chlorophyll a biomass? (2) Does that bump in chlorophyll a get transported downstream? The San Francisco Estuary in California, USA, has a robust and long-term monitoring network for water quality. We integrated water temperature, chlorophyll a, flow, and floodplain inundation data from multiple sources creating a continuous dataset with fine temporal resolution spanning two decades. We used a consistent generalized additive mixed model structure across three regions: the floodplain, the mainstem of the river adjacent to the floodplain, and the section of the river downstream from both the floodplain and mainstem. We found that when the floodplain is not inundated, chlorophyll a biomass is mainly influenced by water temperature. However, when the floodplain is laterally connected during periods of inundation, water spreads over a larger surface area in the floodplain, flows decrease and water temperatures increase creating favorable conditions for chlorophyll a production. High flows during the flood pulse quickly transport chlorophyll a downstream, flushing the estuary with food. Under optimal conditions, tidal mixing in the downstream portion of the estuary can continue to boost chlorophyll a biomass in the system even after the flood waters have retreated. This study can guide the design, enhancement, and management of water conveyance structures to meet environmental flow regulations and to benefit the estuarine food web.