In this study, the diversity and seasonal variation of benthic macro-invertebrates of Bagmati River, Kathmandu, Nepal was studied in 2007 to 2010. Five stations were selected and sampled seasonally and investigated for benthic macro-invertebrates community structure using basic statistical measurement of abundance and diversity indices to characterize the benthic macro-invertebrates. The species richness, evenness and diversity of the benthic macro-invertebrates in the study area were high and typical of a tropical fast-flowing freshwater river. Taxa belonging to 5 invertebrate groups were recorded: insect nymphs/larvae (18 taxa), Oligochaete worms (3 taxa), leeches (3 taxa), snails (2 taxa) and bivalves (1 taxon). Altogether 27 taxa were identified from five sampling sites of Bagmati River. Their population remarkably declined from Gokarna to Chovar. The test indicated that the abundance of Dipterans and Ephemeropterans at station 3, 4 and 5 respectively were the source of the significant (p<0.05) difference.