A declining crocodile population and fish mortalities attributed to pansteatitis, along with increasing blooms of Microcystis aeruginosa and Ceratium hirundinella, have led to serious concerns about water quality in Loskop Dam, on the Olifants River, South Africa. Major impacts include acid mine drainage and eutrophication associated with sewage effluent. However, the specific causes of pansteatitis remain elusive. In 2011 the water chemistry and limnology of Loskop Dam were studied to determine factors that may be influencing aquatic ecosystem health. Long-term monitoring data collected by the Department of Water Affairs were analysed for trends using a seasonal Mann-Kendall trend test, and were used to determine the trophic state of Loskop Dam using the Carlson index. Multiple sites were sampled which showed the reservoir was heterogeneous with regard to nutrient concentrations, algal biomass and dissolved metals. Specifically, the transitional zone was characterised by frequent algal blooms, resulting in fluctuating dissolved oxygen (range = 2.1–14.5 mg/ℓ) and pH (range = 7.35–10.59) levels. Using total phosphorus, Secchi depth, and chlorophyll-a concentrations, the trophic state of Loskop Dam was classified as meso- to eutrophic. Significant positive trends were observed in total (Tau = 0.422) and dissolved inorganic (Tau = 0.193) phosphorus.The reservoir showed a monomictic pattern of summer stratification (October to April) and holomictic winter circulation (June to July), with an increase in the depth and extent of anoxia in the hypolimnion when compared to previous research. Simultaneous elevated concentrations of manganese (>370 μg/ℓ) and iron in near-bottom water samples coincided with hypolimnetic anoxia. Aluminium concentrations exceeded the target water quality range (>10 μg/ℓ) during summer (December) in both surface and near-bottom water samples. We conclude that fish in Loskop Dam are periodically exposed to several physiological stressors including elevated ammonia, aluminium, iron and manganese and possibly hydrogen sulphide, as well as low dissolved oxygen. While these factors have never individually been linked to pansteatitis, their combined impacts have not been studied. To ensure the sustainability of Loskop Dam, catchment management plans must focus on reducing phosphorus inputs, and continue seeking treatment solutions for mine-water associated with abandoned and working coal mines.