Staff of Stillwater Sciences have worked with the Turlock and Modesto Irrigation Districts (collectively "the Districts") since 1986 and have been instrumental in designing and supervising an innovative research program investigating chinook salmon population dynamics in the Tuolumne River below the District-operated New Don Pedro Dam. In order to restore the salmon populations on the Tuolumne River, stakeholders in the settlement negotiation process for the New Don Pedro Project Relicensing were initially focused solely on additional river flows to increases the salmon abundance and were far from agreement on what the appropriate flows should be. Based on a focused, hypothesis-driven study program, Stillwater Sciences worked with the stakeholders to develop a comprehensive understanding of how different causes of mortality throughout salmon life history affected population dynamics. Two types of population models resulted from these scientific analyses. Stillwater Sciences developed a suite of enhancement measures including a tailored flow regime, channel restoration, and experimental measures to reduce predation and redd superimposition, that were incorporated into a successful settlement agreement. The agreed-upon flow regime makes the most effective use of flows and combines the benefits of a revised flow schedule with non-flow measures to increase salmon abundance in the river. This cost-effective salmon enhancement program became the foundation of the first-ever negotiated FERC Settlement Agreement (FSA). The project included population modeling, field research, and field testing of management strategies and became the basis for the Tuolumne River Restoration Plan, encompassing a 1,960-m2 watershed.

Since implementation of the FSA, Stillwater Sciences has worked directly with the Tuolumne River Technical Advisory Committee (TRTAC) and the client to implement the extensive FSA monitoring program. Stillwater Sciences has designed and is conducting studies of fry and juvenile stranding resulting from flow fluctuations, outmigrant survival, and spawning substrate permeability and incubation conditions.

As a result of these efforts and additional studies completed by McBain and Trush, several large restoration projects, funded by CALFED, the AFRP, and the TRTAC, are currently being implemented on the Tuolumne River. The largest projects are channel and floodplain reconstruction at Special Run Pools (SRPs) 9 and 10 and the six-mile-long Gravel Mining Reach. Stillwater Sciences completed the technical analyses and documents required for these projects as part of the Environmental Assessment and Initial Study. Moreover, working with McBain & Trush and the TRTAC, Stillwater Sciences is implementing a monitoring program to assess the effects of the restoration projects on chinook salmon.