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The relationships between water quality and the phytoplankton community within Lake Loskop were studied during the late summer and autumn of 2008 to evaluate the impacts of acid mine drainage and high nutrient concentrations. The higher concentrations of metal ions and sulphate had adverse effects on certain phytoplankton species in the inflowing riverine zone of Lake Loskop, in comparison to the reference site in the lacustrine zone of the lake, which was dominated by the larger and slower growing late summer species of Coelastrum reticulum Nägeli, Straurastrum anatinum Meyen ex Ralfs and Ceratium hirundinella Müller. The high nutrient concentrations (nitrogen: 17mgl−1 and orthophosphate: 0.7mgl−1) during the mid-summer peak of the rainy season were associated with the development of a bloom of the cyanobacterium Microcystis. Water quality data associated with the development of the Microcystis bloom suggest that the aquatic system of Lake Loskop has now entered an alternate, hypertrophic regime. This change overshadowed the adverse effects of high concentrations of heavy metal ions and low pH. Throughout this study, the reference site in the lacustrine zone of Lake Loskop had lower concentrations of metal ions and sulphate, and higher pH values. The response of phytoplankton bioassays on integrated water samples from the different sampling sites did provide potential answers to the reasons for the absence of the algal group Chlorophyceae in the phytoplankton community structure in the riverine zone of the lake. [Copyright &y& Elsevier]