In semi-arid protected areas artificial waterholes ensure that water is locally available to animals for extended periods. However, artificial waterholes may limit animal movement, which contributes towards habitat deterioration. Challenges of artificial water provisioning worsen in the presence of ecosystem engineers like African elephants Loxodonta africana, capable of transforming environments. Camera traps were used to monitor elephant visitation at 21 artificial waterholes in the Kruger National Park, South Africa. We also assessed if water quality parameters influenced elephant preference for certain waterholes. There were no significant correlations between elephant abundance and water physicochemical properties. However, there was a strong negative correlation between elephant abundance and levels of Escherichia coli in water. Our findings suggest that elephants avoid drinking water with high levels of faecal microbial loads. Whereas most studies addressing animal management in protected areas consider waterholes as homogeneous units, we posit that water quality could also determine local landscape use and movement patterns of key species like elephants, a finding with relevant implications in reserve management practices.