The dataset contains concentrations of Total Organic Carbon, Chloride, Fluoride, Bromine, Sulfate, Potassium, Aluminium, Calcium, Iron, Magnesium, Sodium, Phosphorus, Chromium, Manganese, Cobalt, Nickel, Copper, Zinc, Arsenic, Selenium, Molybdenum, Cadmium, Lead and stable water isotopes (δD and δ18O) for 25 groundwater and surface water sampling locations, surveyed over the period February 2017 to May 2018 immediately following Dineo floods. The data were collected as part of the PULA project, which aimed at understanding the immediate effect of heavy rainfall and floods on water resources in arid Botswana and their transitional hydrologic readjustment towards the dry period, and the role of these events in supporting either or both resources replenishment and contamination. The project was co-ordinated by the University of Aberdeen, with partners at the Botswana International University of Science and Technology, the Government of Botswana Department of Water Affairs, and the International Water Management Institute. The project was funded by the Natural Environment Research Council as part of its Urgency grants scheme.