Phytoplankton forms an important trophic level in an aquatic ecosystem and contributes significantly to their primary productivity. The present investigation was carried out on Bhakra-Yamuna link canals at three selected sites (Site S1, S2 and S3) for the qualitative and quantitative analysis of phytoplankton. The constituents monitored were abundance, distribution, total population, group percentage and species diversity of phytoplankton for one year (January-December, 2013).Shannon diversity index (2.47 to 3.29) and species evenness (0.71 to 0.93) were higher at site S2 indicating high diversity and lower (1.58 to 2.42) at site S1. Phytoplankton density showed maximum values at site S2 and S3 as compare to site S1.Species richness, population density and mean values of Shannon diversity index of phytoplankton show decrease in their values at site S3 after linking with site S1. Jaccard’s similarity coefficient calculated on the basis of phytoplankton revealed that site S2 and S3 was more similar as compare to site S3& S1 and site S1& S2 throughout the study period. Oscillatoria sp., Scenedesmus sp. and Spirulina sp. were dominant at site S1 while at site S2 green algal flora like Spirogyra sp. and Zygnemasp. showed abundance.