Small aquatic ecosystems in semi-arid environments are characterised by strong seasonal water level fluctuations. In addition, land use as well as artificial pumping of ground water to maintain water resources throughout the dry season may affect the functioning of aquatic ecosystems. In this study, we investigated pans situated in and around Hwange National Park, Zimbabwe, where certain waterholes are artificially maintained during the dry season for conservation purposes. We monitored 30 temporary and permanent waterholes for seven months across the wet and dry seasons in 2013 and analysed them for standard parameters to investigate seasonal variations, assess the effects of land use and pumping on lake functioning, and determine the driving factors of these aquatic systems. Results show an increase in conductivity, hardness, and turbidity when temporary pans dry up and permanent ones are filled with ground water. Prominent parameters explaining the diversity of aquatic ecosystems are water hardness, conductivity, turbidity, and the presence of vegetation. Seasonality differences in certain parameters suggest the influence of water level fluctuations associated with rainfall, evaporation, and pumping activities. Further, the distinction between turbid pans and those with clear water and vegetation suggests the alternative functioning of pans. Land use had no significant effects, while the effects of pumping are discussed. In times of water scarcity, animals gather around artificially maintained waterholes and foul water with faeces and urine, thus inducing water eutrophication.