Water year types (WYTs), whereby years are classified by river runoff quantity compared to historical runoff, are one tool to help make major water management decisions. Increasingly, these decisions include instream flow requirements (IFRs) below dams for river ecosystem management. However, WYTs are typically based on assumptions of stationarity, and are thus rendered less meaningful with climate change. Hydrologic alteration resulting from climate change means that a WYT-based IFR scheme using stationary historical observations might inadvertently result in long-term river management outcomes inconsistent with original water management goals. This study assesses the management implications of assuming hydrologic nonstationarity in a WYT-based IFR scheme in California’s upper Yuba River and demonstrates a rolling period of record as a climate adaptation strategy. The existing, nonadaptive water management scheme leads to vastly different possible water allocation outcomes than originally planned for. Results indicate that water year types, if regularly updated, can help maintain historical instream flow distributions. However, gains toward maintaining desired IFRs are obfuscated by future increases in unmanaged reservoir spill. These findings indicate that hydroclimatic uncertainty can partially be accounted for with simple modifications to existing operating rules for reservoirs, though other, risk-based management approaches are also likely needed.