Stable carbon (δ¹³C) and oxygen (δ¹⁸O) isotope measurements in lacustrine ostracodes are widely used to infer past climatic conditions. Previous work has used individual ostracode valves to resolve seasonal and subdecadal climate signals, yet environmental controls on geochemical variability within co-occurring specimens from modern samples are poorly constrained. Here we focus on individual ostracode valves in modern-aged Lake Turkana sediments, an alkaline desert lake in tropical East Africa. We present individual ostracode valve analyses (IOVA) of δ¹³C and δ¹⁸O measurements (n = 329) of extant species Sclerocypris clavularis from 17 sites spanning the entire lake (n-avg ~19 specimens per site). We demonstrate that the pooled statistics of individual valve measurements at each site overcome inter-specimen isotopic variance and are driven by hydrological variability in the lake. Mean IOVA-δ¹³C and -δ¹⁸O across the sites exhibit strong spatial trends with higher values at more southerly latitudes, modulated by distance from the inflow of the Omo River. Whereas the latitudinal δ¹³C gradient reflects low riverine δ¹³C and decreasing lacustrine productivity towards the southern part of the lake, the δ¹⁸O gradient is controlled by evaporation superimposed on the waning influence of low-δ¹⁸O Omo River waters, sourced from the Ethiopian highlands. We show that ostracode δ¹⁸Oproximal to Omo River inflow is deposited under near-equilibrium conditions and that inter-specimen δ¹⁸O variability across the basin is consistent with observed temperature and lake water δ¹⁸O variability. IOVA can provide skillful constraints on high-frequency paleoenvironmental signals and, in Omo-Turkana sediments, yield quantitative insights into East African paleohydrology.