Rivers feeding into the Loskop Dam, South Africa, pass through coal mining and heavily industrialised areas. Previous studies investigating mass mortalities of crocodile and fish in the river system, revealed the presence of organic compounds, including polycyclic aromatic hydrocarbons (PAHs), in their tissues. Samples were collected from nine sites within the dam in winter and summer. Liquid-liquid and microwave-assisted extraction was used for preconcentrating PAHs from water and sediment samples, respectively. Extracts were analysed by gas chromatography-mass spectrometry in the selected ion monitoring mode to determine the presence and levels of the 16 United States Environmental Protection Agency (US EPA)-priority PAHs. Significant levels of PAHs were found in both water and sediment samples. Concentrations were higher in sediments than in water, as well as in samples collected in winter. Levels of PAHs in sediments were generally higher than those reported by many researchers for other water bodies in industrialised areas. Zebrafish embryos were used to assess potential risks associated with the water and sediment, and to determine the effects of PAHs on aquatic life. Embryos, exposed to intact water and sediment samples, as well as to diluted sediment extracts, were monitored for 120 h post fertilisation. Sediment proved more toxic to zebrafish embryos than water, causing delayed embryo development and malformations. These findings are alarming as they indicate that this water system is under stress. These findings can be typical of any water system situated in a coal mining and industrial region.