Rivers are vulnerable to eutrophication as a result of increased deposition of nutrients from human activities taking place within watersheds. Uncontrolled release of nutrients into these important freshwater ecosystems can compromise water quality status for domestic consumption and create unfavourable habitat conditions for aquatic biota. This study investigated the seasonal fluctuations in the levels of nitrate-nitrogen and phosphate-phosphorus at various land uses in River Isiukhu, Kenya from January to June 2013. Land use significantly impacted on phosphate-phosphorus (F=11.1, p<0.05) and nitrate-nitrogen concentrations (F=13.7, p<0.05). The forest land use recorded the lowest concentration of nitrate-nitrogen (2.24 Mg L-1) and phosphate-phosphorus (0.07 Mg L-1) while the mixed agricultural land use recorded the highest level of the two nutrients i.e. (5.7 Mg L-1) and (0.2 Mg L-1) respectively. Nutrient concentrations increased in river sections with high intensity of human activities and increased destruction of the riparian vegetation. The concentrations of the two nutrients studied varied with the changes in the amount of rainfall received in the watershed. The lowest concentrations of the two nutrients were observed in February 2013 when only 32.5 mm of rainfall was received while the highest concentrations occurred in April at the peak of the rainy season. Spearman rank order correlation revealed positive correlations between the amount of rainfall and the concentrations of nitrate-nitrogen and phosphate-phosphorus. From this study, it is recommended that there is need to regulate the nature of human activities taking place in the riparian areas due to the potential impact of these activities on nutrient levels.