We investigated the spatial and temporal variations of the stable isotope composition of hydrogen (δD) and oxygen (δ18O) and the total dissolved ions (TDI) concentrations in the Okavango River flowing through the Okavango Delta (Delta) in the middle Kalahari Desert. We aimed to elucidate the role of evaporation in controlling river solute enrichment from water samples collected at a one- to two-month frequency from nine stations along a ~460 km river transect for one year. We found that the δD and δ18O composition and the TDI concentrations increased downriver. Seasonal increases in the δD and δ18O composition and in the TDI concentrations during the hot, rainy season were subdued and decreased during the cool, dry season from pulse flooding. The δD and δ18O composition of the river samples plot along the Okavango Delta Evaporation Line are consistent with evaporation. The effect of evaporation during river transit was related to the mean δD (δD = 0.07*River distance (km) – 37.9; R2 = 0.98) and mean d-excess (d-excess = -0.04*River distance (km) + 9.9; R2 = 0.94). The effect of evaporation on the river solute behavior was characterized by the mean d-excess and TDI concentrations (d-excess = -0.29*TDI (mg/L) + 15.0; R2 = 0.97). Samples from this study and those compiled from published studies plot at greater than one sigma standard deviation above and below the mean TDI concentration vs. mean d-excess regression model line. We use the marked deviations from the mean TDI concentration vs. the mean d-excess regression model to suggest that additional solutes from river-floodplain-wetland-island interaction driven by pulse flooding are delivered into the river. While our findings support an evaporation-dominated solute enrichment during river transit at the seasonal scale, we conclude that intermittent hydrology (e.g., pulse flooding) plays an important role in the sub-seasonal spatiotemporal behavior of solutes in rivers in arid watersheds, which must be considered in solute cycling models.