Multivariate statistical analysis was used to identify the main contaminants in the river at the various sections of the river. The results obtained indicated that species richness and diversity are high during low flow condition and the lower reaches had high species richness and diversity compared to the middle and upper reaches. The Fish Response Assessment Index indicated that the Ecological Class for the Crocodile River is mostly at C class beginning from the Kwena Dam downstream. Water quality constituents such as total dissolved solids and electrical conductivity increase with the increase in river distance in the downstream reaches.