In late December 2025, a series of storms swept through Northern California, causing the Sacramento River to rise rapidly. By December 29, the river levels were sufficient to cause the Fremont Weir to overflow. This event marked a significant milestone: the overtopping of the two-mile-long weir coincided with the first operational activation of the Big Notch Project gates, an upgrade to the Fremont Weir designed to allow managers to control water flow from the Sacramento River into the Yolo Bypass earlier and more efficiently. Unlike the solid wall of the original weir, these gates allow water to flow into the Yolo Bypass at lower river elevations, before the river reaches the 32-foot flood stage. This engineering change transforms the weir from a strictly passive flood barrier into a managed diversion facility.
“This is an updated engineering of the weir that gives managers more choices,” Delta Lead Scientist Dr. Windham-Myers told the Delta Stewardship Council at their January meeting. “It improves flood control. It provides fish pathways for big fish like salmon and sturgeon, and it demonstrates the multiple benefits of floodplain connectivity to the Delta community.”
The main purpose of the Big Notch Project is to improve flood safety while also delivering ecological benefits. The project is designed to allow water onto the Yolo Bypass floodplain more frequently and for longer periods. This action mimics the historical flooding patterns that native fish populations, particularly juvenile salmon, depend on for a nutrient-rich habitat before they migrate to the ocean.
To illustrate this, Dr. Windham-Myers spotlighted a recent, peer-reviewed study that confirms the ecological value of such floodplain inundation. The paper, Floodplain inundation and lateral connectivity promote productivity in a managed river system, published in Ecological Applications, analyzed over two decades of data, including water temperature, chlorophyll a, flow rates, and floodplain inundation, to determine where, when, and how the Yolo bypass floodplain supports primary production and nutrient transport during high flows. These insights are critical to designing and managing water conveyance structures and flow regulations in the Delta.
The researchers developed a model showing how rewetting floodplains disconnected from the river can boost phytoplankton growth and ultimately inject more food into the river system.
The conceptual diagram shows how it works. As shallow water spreads across the inundated floodplain, sunlight penetrates, and temperatures rise. This stimulates phytoplankton growth, which is then flushed downstream from the floodplain during periods of high flow or as the flooding recedes. Tidal mixing at the confluence keeps phytoplankton in the Delta rather than flushing them out to sea, which helps support aquatic food webs within the Delta.
“The key takeaway of the paper is that restoring river floodplain connectivity boosts primary productivity and enhances downstream food webs. Scientists often liken our Delta channels to food deserts. So improving connectivity in systems like ours is crucial for the Delta ecosystem, health, and proper design and operation of structures like Big Notch in Fremont Weir can aid this effort by being able to control nimbly when flooding is occurring and how much.”
The work was made possible by the Delta Science Program’s collaboration with the National Center for Ecological Analysis and Synthesis (NCEAS). NCEAS facilitates data science training for scientists to build foundational skills in data science and statistics, and to gain new insights from the exploration and synthesis of long-term monitoring data from Delta sampling programs.
Dr. Windham-Myers concluded by highlighting that two decades of data collection underscore the vital role of lateral connectivity in transforming floodplains into essential habitats and food sources for native species.
“Documenting this requires collaboration to quantitatively show it, which generates confidence in understanding the cobenefits of different management options,” she said. “We can expect to see more synthesis products coming out of our NCEAS cohorts.”
RESEARCH PAPER: Floodplain inundation and lateral connectivity promote productivity in a managed river ecosystem
By: Shruti Khanna, Catarina Pien, Pascale Goertler, Lauren Yamane, Elizabeth Stumpner, Jereme William Gaeta, Dylan Chapple, Mattea Berglund, Ryan Peek
Abstract: 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.
Click here to read this open access paper.
