Benthic macroinvertebrate communities are frequently applied as indicators of aquatic ecosystem health as many species are responsive to pollution and abrupt changes in their surroundings. The qualities of benthic invertebrate communities greatly depend on habitat conditions. Thus the diversity in benthic community varies with different habitat conditions. This investigation on the structure of the benthic invertebrate communities was conducted on river Ichamati, a trans-boundary river between India and Bangladesh to assess the cumulative effects of water quality on the aquatic biota. The study period extended from February 2011 to January 2014 at three sites from Majdiah to Hasanabad (in West Bengal, India) a stretch of 124km. A total of 23 macrobenthic species belonging to three phyla, five classes and nine orders were identified. Fifteen species of benthic invertebrates belonging to Mollusca, three species under Annelida and five species under Arthropoda were found. The highest abundance density (3633.33 indiv.m-2) and species richness (18 species) were recorded up-stream (Majdiah) where marginal habitats covered by macrophytes were significantly higher than at other sites. Both the organic carbon (4.41±1.11) and organic matter (7.48±1.56) of soil at this site were the maximum thus influencing the richness of benthic macroinvertebrate communities. Hydrological variables, viz, dissolved oxygen, pH, alkalinity; hardness, salinity, nutrients, calcium, and magnesium were studied to determine their influences on the benthic community in the upper, middle- and down-streams of the river, respectively. Shannon’s diversity index (0.95–2.07; 0.00–0.72; 0.00–0.64), dominance index (0.57–0.86; 0.00–0.44; 0.00–0.44), evenness index (0.72–0.95; 0.61–1.00; 0.00–1.00), Margalef index (0.72–2.23; 0.00–1.32; 0.00-0.28) of the upper, middle- and down-streams were calculated. Benthic macroinvertebrate density was correlated with hydrological variables which indicated that the abiotic factors had either direct or inverse influence on the richness and abundance; however, the abiotic factors did not correlate identically in all three sites.