TO: Technical Advisory Group for the Napa County Groundwater Sustainability Agency
FROM: Brian D. Bordona, Director of Planning, Building and Environmental Services
REPORT BY: Jamison Crosby, Natural Resources Conservation Manager
SUBJECT: Update on the Interconnected Surface Water (ISW) Groundwater Dependent Ecosystems (GDEs) Workplan implementation and on the California Environmental Flows Framework (CEFF) assessment
RECOMMENDATION
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Receive an update on the Interconnected Surface Water (ISW) Groundwater Dependent Ecosystems (GDEs) Workplan implementation and the California Environmental Flows Framework (CEFF) assessment.
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Procedure
Staff introduces.
Questions and answers with the TAG.
Public comments.
BACKGROUND AND DISCUSSION
A fundamental knowledge gap in setting sustainable management criteria in the Napa Valley Groundwater Subbasin (Subbasin) is understanding the spatial and temporal flow requirements of sensitive species. To fill this knowledge gap, the Napa County Groundwater Sustainability Agency implemented the Interconnected Surface Water (ISW) and Groundwater Dependent Ecosystems (GDEs) Workplan (Workplan) starting in 2024. The Workplan includes field investigation of the timing and usage of the Subbasin by special status fish, amphibians, and reptiles at six sites including four sites on the mainstem Napa River (Calistoga, St. Helena, Yountville, and Oak Knoll) and two tributaries (Sulphur Creek and Bale Slough). California freshwater shrimp (Syncaris pacifica) surveys were limited to the Napa River at Calistoga, which is within the critical habitat area for the species. Biological surveys also included riparian GDEs including vegetation and birds. In addition to biological surveys, the Workplan also called for monitoring of shallow groundwater, surface water stage, wet-dry mapping, water temperature, and dissolved oxygen.
Following the Groundwater Sustainability Plan for the Subbasin, the Workplan recommended using the California Environmental Flows Framework (CEFF) to develop scientifically defensible environmental flow criteria and inform sustainable management criteria. The CEFF assessment focused on spring recession and dry-season baseflow periods when flows are most sensitive to groundwater extraction and most important for sustaining ecological functions in the subbasin. The CEFF assessment presented to the Technical Advisory Group focuses on the scientific portions of CEFF (Sections A and B). Section C, which balances the needs of various water users in the development of flow recommendations and implementation strategies, will be addressed in 2027.
Section A focuses on developing ecologic management goals and hydrologic analyses of unimpaired flows. The ecological management goals varied by site but focused on maintaining or enhancing aquatic habitat for special-status species with a focus on lifestages that currently use the site. For example, maintaining or enhancing foothill yellow-legged frog (Rana boylii) habitat is a management goal for Sulphur Creek and the Napa River at St. Helena, the two sites where they were observed. Hydrologic analyses used the California Natural Flows Database (CNFD), long-term USGS streamflow records, field monitoring, wet-dry mapping, biological surveys, and the Napa Valley Integrated Hydrologic Model (NVIHM). The NVIHM and CNFD were used to explore the magnitude and timing of spring recession and dry-season baseflow in the absence of groundwater pumping. These models suggest that groundwater pumping has relatively little influence on spring recession timing and duration but substantially affects dry-season baseflows in the mainstem Napa River. NVIHM suggests that, on average, groundwater pumping reduces dry-season flows by approximately 5 cubic feet per second (cfs) at St. Helena and about 10 cfs at Oak Knoll. Stream depletion effects are greatest during summer, when groundwater contributions become critical to sustaining flow and connectivity. The NVIHM and shallow groundwater monitoring suggest that groundwater pumping does not affect spring recession or dry-season baseflow in Sulphur Creek or Bale Slough.
The final part of the Section A assessment identified widespread non-flow stressors, including channel incision, floodplain disconnection, habitat simplification, degraded water quality, elevated stream temperatures, low dissolved oxygen, invasive species, and legacy effects of channel modification and gravel mining. These factors often limit habitat quality regardless of flow conditions, especially in mainstem reaches, suggesting that a Section B analysis was required to assess flow-habitat requirements for the species of interest.
Section B of the CEFF assessment focused on developing flow-habitat relationships for steelhead (Oncorhynchus mykiss) and foothill yellow-legged frog because their life histories are strongly linked to spring recession flows and summer baseflows. Foothill yellow-legged frogs breed and deposit eggs along channel margins, where velocities are sufficiently low during spring recession. Tadpoles subsequently emerge and monitoring at Sulphur Creek suggests that tadpoles metamorphose into adults by June or early July. Tadpole development does not have minimum flow requirements but requires wet conditions. Because metamorphosis can occur in June, early dry-season baseflows are crucial for tadpole development. Once the tadpoles metamorphose into sub-adult frogs, they can leave the stream and rely on other sources of water.
Monitoring showed that the Napa River primarily functioned as a migration corridor for steelhead, with limited evidence of successful juvenile rearing mostly due to elevated summer stream temperatures, low dissolved oxygen, and seasonal loss of connectivity. Young-of-the-year steelhead were observed in June at the Sulphur Creek site in 2024 and 2025 and the Napa River at Calistoga in 2024 but were otherwise only observed in small numbers. Subsequent to the surveys, Sulphur Creek went dry and the Napa River at Calistoga transitioned to isolated pools. At all of the sites, either temperature or dissolved oxygen were stressful for fish during the dry season, likely limiting their usage as rearing habitat, likely due to wide, open channel morphologies and lack of riparian shade. Based on data available to date, recommendations focus on supporting movement to locations where habitat conditions are more suitable, which include potential temperature refuges within the mainstem or downstream at the Napa-Sonoma marshes. Based on NVIHM model simulations and Stream Watch data, tributaries become disconnected from the mainstem Napa River in June or as late as July. Once the tributaries become disconnected from the mainstem intra-basin movement is less important. However, while the tributaries are connected, ecological management objectives focus not only on maintaining flow but also on preserving seasonal connectivity, supporting species movement and recruitment, and sustaining critical habitats such as isolated pools and cool-water refugia. Foothill yellow-legged frog metamorphosis and the transition of tributaries to isolated pools (thus limiting intra-basin movement) both occur in June or early July, on average.
The CEFF analysis recommends maintaining sufficient flow in June for the Napa River mainstem to support steelhead migration and foothill yellow-legged frog metamorphosis. Spring and early summer flows in Sulphur Creek and Bale Slough depend on surface water inflows to the Subbasin rather than groundwater management.
While foothill yellow-legged frog tadpoles require wet conditions, they do not have minimum flow requirements. In contrast, a minimum flow depth of 0.3 ft is required for young-of-the-year steelhead migration and 0.4 ft for older juvenile migration. Where both migrating steelhead and foothill yellow-legged frogs occur, steelhead can be used to assess minimum flow needs because their flow requirements are greater. Defining the flows at which passable conditions occur is a key next step in developing interconnected surface water sustainable management criteria.
Although relationships between groundwater elevation, discharge, and flow depth are sparse, flow depths were recorded during the habitat mapping surveys conducted as part of Workplan implementation. Although these data only provide one discharge-flow depth data point per site, they can be used to provide a preliminary estimate of flow requirements. At St. Helena, flow depth at riffle crests was less than 0.3 ft, at discharge of 2.8 cfs in June 2024, suggesting that the minimum passage flow was higher. At Oak Knoll, flow depth exceeded 0.4 ft in July 2025 at a discharge of 10.5 cfs, suggesting that 10.5 cfs is suitable for passage of juvenile salmonids. The 2025 observation at Oak Knoll was influenced by beaver dams.
Refining the flows required for migration requires developing relationships between discharge and flow depth over shallow areas (riffles) at the intensive sites to determine the discharge necessary for various lifestages of steelhead to migrate to more suitable habitat. The study concludes that, while management of groundwater resources can improve dry-season connectivity in portions of the mainstem Napa River, long-term ecological benefits will also depend on addressing habitat and water-quality limitations. Continued monitoring, hydraulic analyses, and improved understanding of groundwater-surface water interactions are recommended to refine ecological flow criteria and support sustainable groundwater management throughout the Napa Valley Subbasin.
ENVIRONMENTAL IMPACT
ENVIRONMENTAL DETERMINATION: The proposed action is not a project as defined by 14 California Code of Regulations 15378 (State CEQA Guidelines) and therefore CEQA is not applicable.
SUPPORTING DOCUMENTS
A. Napa California Environmental Flows Framework Assessment Progress Update (Stillwater Sciences, September 2026)