Degradation of water resources due to anthropogenic activities is a major problem all over the world. Monitoring changes in water quality is expensive but essential for management of water resources. Diatom assemblages can serve as useful indicators of changes in water quality. In order to determine changes in stream water quality in an urban environment, densities of epilithic diatom communities on both natural and artificial substrates were sampled in Nairobi River, Kenya in September 2000. Sampling of water and diatoms was carried out in almost equidistant sites along a 60 km stretch of the Nairobi River. Environmental (water physico-chemical and nutrients) data was explored by Principal Correspondence Analysis (PCA) and sites split into three groups of upper-, mid- and lower stream. Most abundant diatom taxa on both substrates were selected and their relationship with environmental variables determined. On artificial substrates, Gomphonema parvulum , Nitzschia palea and Nitzschia umbonata were the most abundant and were significantly related with total dissolved solids, nitrate, conductivity and turbidity. Temperature, altitude and pH interacted significantly with dominant diatom species on natural substrates, which included Gomphonema parvulum , Nitzschia palea and Navicula subminuscula . Non-parametric analyses showed that diatom densities in natural and artificial substrates were significantly different and were affected by different environmental variables. Our results indicate that abundant diatom species can be used to describe major types of aquatic environmental gradients and can serve as good indicators of ecological conditions in tropical streams and rivers. This study also showed that diatoms from artificial and natural substrates can be used to provide complementary information.