Benthic macroinvertebrates from Rivers Kipkaren and Sosiani in the upper reaches of River Nzoiabasin, Kenya, were sampled semi-quantitatively monthly from December 2006 to May 2007 using a0.5 mm mesh size scoop net in the riffles, pools and runs. Seven sampling sites were selected on theareas of the rivers along a longitudinal gradient in relation to anthropogenic impact. Physicochemicalparameters were measured in situ, while specific chemical parameters were determinedcalometrically in the laboratory using standard methods. Habitat and land use characteristics werealso recorded. A total of 1499 macroinvertebrates belonging to 13 orders, 28 families and 31 generawere collected. The orders Ephemeroptera, Hemiptera and Coleoptera were taxonomically richest.Overall, a total of 31 genera for River Kipkaren dominated by the EPT and 19 macroinvertebrategenera for the lower River Sosiani dominated by dipterans were recorded. Conductivity, oxygen andtotal nitrogen varied significantly (p < 0.05) between sampled sites, but not temporally. The results ofredundancy analysis using 9 dominant macroinvertebrate genera revealed a distinction betweenimpacted and the less impacted sites and the physico-chemical parameters associated with thisdistinction.