The annual flood pulse in the Okavango Delta (Botswana), has a major influence on water chemistry and habitat. We explore spatial and temporal patterns in a suite of chemical variables, analysed from 98 sample points, across four regions, taken at different stages of the flood cycle. The major pattern in water chemistry is characterised by an increasing gradient in ionic concentration from deepwater sites in the Panhandle to more shallow, distal regions to the south. Concentrations of cations, anions, dissolved organic carbon, and SiO 2 are significantly higher in the seasonally inundated floodplains than in permanently flooded regions. Several variables (including Na and total nitrogen) significantly increase from low flood to high flood, while others (including HCO 3 , SiO 2 , and Cl) increase in concentration, initially between low flood and flood expansion, before declining at maximum flood extent. Redundancy analysis (RDA) revealed that hydrological variables (water depth, flow velocity, flood frequency, and hydroperiod class) significantly explain 17% variation in surface water chemistry. Predictions of increasing flood volume in the near future may result in a decline in alkalinity and dilution of DOC. Our study provides an important baseline from which to monitor future change in the Delta.