Increasing demands for water, discharge of effluents, and variable rainfall have a negative impact on water quality in the Olifants River. Crocodile and fish mortalities attributed to pansteatitis, in Loskop Dam and downstream in the Kruger National Park (KNP), have highlighted the serious effects these impacts are having on aquatic ecosystems. Flag Boshielo Dam is a reservoir on the Olifants River, located between Loskop Dam and the KNP. It has the largest crocodile population outside of the KNP, and pansteatitis has not been reported in fish or crocodiles to date. This study evaluated comparative water quality parameters concurrent to a similar study undertaken at Loskop Dam to establish possible environmental drivers of pansteatitis. Long-term monitoring data collected by the Department of Water Affairs were analysed for trends using a Seasonal-Kendall trend test. Short-term monitoring showed that water quality in Flag Boshielo Dam was of a good standard for ecosystem health. Concentrations of dissolved Cu, Se, V and Zn were always below instrument detection limits, and Al, Fe and Mn were mostly within guideline levels for ecosystem health. A severe drought occurred between November 2002 and December 2005. Long-term monitoring showed that water quality during the drought deteriorated, with high levels of dissolved salts, especially K, Na, Cl, F, and total alkalinity. Following the drought, dissolved salt concentrations dropped, and there was a brief flush of inorganic N and P. However, between 1998 and 2011, inorganic N showed a significant decreasing trend into the oligotrophic range, while inorganic P remained in the oligo- to mesotrophic range. The inorganic N to inorganic P ratio of 5.4 after the drought was indicative of N limitation, and the phytoplankton assemblage was dominated by nitrogen-fixing species, especially Cylindrospermopsis sp. In contrast, further upstream, Loskop Dam has undergone increasing eutrophication, has frequent blooms of Microcystis aeruginosa and Ceratium hirundinella, and concentrations of Al, Fe and Mn periodically exceed guideline levels. The difference in trophic state, phytoplankton assemblage and levels of productivity between these two reservoirs may provide insights into the aetiology of pansteatitis, which is frequently associated with dietary causes.