A baseline study was conducted of the occurrence of macroinvertebrates at 26 sites in the Nyando River catchment in 2005-2006. A total of 13 orders and 16 families of Arthropoda, Mollusca, Platyhelminthes and Annelida were collected, with the order Ephemeroptera being most abundant in the up- and mid-stream reaches, followed by Hemiptera and Plecoptera respectively. The downstream sections of the river were dominated by Hirudinea and tubificids, as the water quality deteriorated mainly due to local land use, raw sewage effluent discharge and annual floods. Insects and annelids were the main invertebrates found and the extent of pollution increased from mid-section (Site 15) downwards as the river flowed into the Winam Gulf. Stringent management measures are required to safeguard the environment and ecosystems of Lake Victoria.