The consequences of acid mine drainage (AMD) are apparent in water and sediment of the upper reaches of the Crocodile River (West) system, which is located in the western basin of the Witwatersrand mountain chain in South Africa. Another significant indicator for metal and metalloid pollution in aquatic systems is biota. In particular, in the case of AMD-impacted areas, which occur worldwide, biota could serve as an important bioindicator of contamination and also be useful in terms of remediation of pollutants. We investigated the content of Fe, Ni, Cu, Zn, As, Se, Ag, Cd, Hg, and Pb in the liver and muscle tissue of 4 fish species (Oreochromis mossambicus, Labeobarbus polylepis, Labeobarbus marequensis, and Clarias gariepinus) and in roots and stems of macrophytes Pontederia crassipes, Typha sp. and Phragmites australis taken from selected sites in the system. Metals and metalloids were analyzed in freeze-dried and acid-digested samples using graphite furnace atomic absorption spectroscopy, cold vapor atomic absorption spectroscopy, and total reflection X-ray fluorescence spectroscopy. We determined that the mean levels of Fe, Ni and Cu were increased in the roots of Typha sp. and P. crassipes at sites influenced by AMD. Both macrophytes could also be used for phytoremediation of Ni, Cu and Cd, with bioaccumulation factors above 1 at all study sites ranging from 1.1 (Cu) to 21 (Cd) for Typha sp. and 2.7 (Ni) to 25 (Cd) for P. crassipes. Plants were found to be better bioindicators for AMD than fish due to homeostatic regulation of Ni, Cu, and Zn in fish at chronic low-level pollution. An exception was the liver tissue of O. mossambicus, which accumulated high levels of Ni (2.98 ± 1.24 mg kg⁻¹ dw), Cu (184 ± 124 mg kg⁻¹ dw) and Ag (2.01 ± 0.51 mg kg⁻¹ dw), demonstrating its bioindicative potential for these metals. Our study allowed a detailed look at an AMD influenced river system, revealing results that clearly demonstrate the consequences of chronic low-level pollution, although water melioration is in place.