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This study quantified climatological and hydrological trends and relationships to presence and distribution of 2 native aquatic species in the Kansas River basin over the past half century. Trend analyses were applied to indicators of hydrologic alteration (IHAs) at 34 streamgages over a 50-year period (1962-2012). Results showed a significant negative trend in annual streamflow for 10 of 12 western streamgages (up to -7.65mm/50years) and smaller negative trends for most other streamgages. Significant negative trends in western basin streamflow were more widespread in summer (12 stations) than in winter or spring (6 stations). The negative-trend magnitude and significance decreased from west to east for maximum-flow IHAs. Minimum-flow IHAs, however, significantly decreased at High Plains streamgages but significantly increased at Central Great Plains streamgages. Number of zero-flow days showed positive trends in the High Plains. Most streamgages showed negative trends in low- and high-flow pulse frequency and high-flow pulse duration, and positive trends in low-flow pulse duration. These results were consistent with increasing occurrence of drought. Shift in occurrence from present (1860-1950) to absent (2000-2012) was significantly related (p<.10) to negative trends of 1-day maximum flows (both species) and indices associated with reduced spawning-season flows for Plains Minnow and shifting annual-flow timing and increased flow intermittency for Common Shiner. Both species were absent for all western basin sites and had different responses to hydrological index trends at eastern basin sites. These results demonstrate ecohydrological index changes impact distributions of native fish and suggest target factors for assessment or restoration activities.