AbstractStable carbon (δ13C) and oxygen (δ18O) isotope measurements in lacustrine ostracodes are widely used as paleolimnological indicators of past climate change. Previous work has used individual ostracode valves to resolve seasonal and subdecadal paleohydrological signals, yet replicated assessments of co‐occurring specimens from modern samples are rare. Here we focus on ostracodes from sediments collected in 1979 from Lake Turkana, an alkaline desert lake in tropical eastern Africa. Sourced from the Ethiopian highlands, the Omo River is the dominant inflow into this lake. We present individual ostracode valve analyses (IOVA) of δ13C and δ18O measurements (n = 329) of the extant benthic ostracode Sclerocypris clavularis from 17 sites spanning the entire lake (navg = ∼19 specimens/site). We demonstrate that the pooled statistics of individual valve measurements at each site are shaped by lake hydrology, superimposed over inter‐individual isotopic variations. Within‐site variance in IOVA‐δ13C is larger (∼60%) than that of IOVA‐δ18O. Yet, site‐based averages exhibit a systematic pattern, with higher δ values toward the southern part of the lake, away from Omo River inflow. We suggest that the latitudinal δ13C gradient may arise from low riverine δ13C and low organic matter δ13C as a productivity response to nutrient‐rich Omo River inflow toward the north. The δ18O pattern may be explained by the diminishing influence of Omo River inflows and more evaporation driving higher IOVA‐δ18O values toward the windier, southern basin. We conclude that pooled IOVA statistics in Omo‐Turkana sediments can aid interpretations of past regional paleohydrology and its variability in this basin.