The present study was carried out in the lower middle Western Himalayan streams in the Indian state of Himachal Pradesh of the three river basins namely the Ghaggar, the Sutlej and the Yamuna. The main aim was to study fish assemblage structure/composition, fish diversity in different habitats and the habitat preference of the fishes. The different habitats like pools, riffles, runs and rapids were sampled over a 2 km stretch at all the sites with the help of cast net of 1 cm mesh size having a diameter of 1-2 meter on a fixed day every month between mid morning and late afternoon. All the sites when broadly delineated at level-1 fall into type - B except site II that is an F - type stream. A total of 23 species belonging to four orders were recorded of which the cyprinids were the most dominant group. According to Shannon-Weawer diversity index, the pool habitat supports greater diversity (H' = 0.72-0.97), Runs (H' = 0.24-0.87) and riffles (H' = 0.22-0.81) have diversity very near to each other at all the sites whereas rapids have significantly lower fish diversity (H' = 0.00-0.58). The pool is the preferred habitat for most of the cyprinid fishes recorded in the present study especially the minnows.