The present study aims to assess the relationship between water quality and macrophytes biomass of KongbaRiver, Manipur (Latitude 25.800 N to 25.680N and 93.030E to 94.780E longitude). Pearson correlation (r) testwas carried out to identify the association between water quality for sampling sites and the Macrophytes biomass. The analysis indicated that D.O is correlated negatively with all the macrophytes biomass. However,the values of nitrate and phosphate were positively correlated with the macrophytes biomass. Water qualitywith regard to temperature, pH, DO, Cl, Ca, Mg, Hardness, Alkalinity, NO3 andPO4 were analysed. Thepresent communication reflects seasonal variation of water quality in the river. Seasonal variation in biomassof macrophytes functional groups were estimated from the five study sites. Macrophytes biomass exhibitedthe trend as E>FF>Sub>RF in site (II, III, IV and V)whereas in site I macrophytes biomass was observed asE>Sub>RF>FF. The study reveals that the water quality ofthe Kongba River were found to be related tomacrophytes biomass either positively or negatively but the nutrients levels were within the normal rangefor macrophytes growth. Concentration of morenutrients in the water bodies can lead to eutrophicationand results in macrophyte bloom. Therefore, there is need to monitor and check the water quality at regularintervals and the growth of macrophytes to ensure the healthy development and maximum production ofbiomass.