Water year indices and drought indices are helpful for categorizing water years into similar types, allowing water managers and policymakers to quantify years, visualize variability, and guide water operations. Many water management decisions, such as environmental flow requirements and water supply allocations, are based on water year type designations. They vary by region and index, but are defined by runoff in the current water year compared to average historical runoff, with numerical thresholds categorizing year types. California's Sacramento Valley and San Joaquin Valley Indices are used as case studies to examine how climate change affects indices. Modeled streamflow for 1951–2099 from the climate-forced Variable Infiltration Capacity hydrologic model estimate potential changes in runoff and water year type frequency. We show that the frequency of water year types changes significantly with climate change and different strategies to adapt water year classification indices to climate change affect water allocations as much as the impacts from changing hydroclimatic conditions.