The Alibori River, which flows through Benin’s cotton crop regions, receives surface water from much of the cultivated land that is situated along its banks. Chemical pollution in surface runoff from this land use threatens the ecological quality of the river. This study aimed to characterise the ecological status of the Alibori River under such agricultural pressures using biological indices and macroinvertebrate metrics. Water and macroinvertebrate samples were taken monthly from fifteen sites along the river between June 2015 and May 2016. The measured physico-chemical parameters and biological indices were subjected to descriptive statistics, bivariate correlations and partial least squares regression (PLSR). Taxonomic richness decreased from the upstream to the downstream reaches of the river. Sampling sites with high mineral content and organic load were home to more pollutiontolerant taxa, such as Chironomidae and Oligochaeta, with a high abundance of Thiaridae. Diversity indices reveal an unbalanced community and macroinvertebrate distribution characterised by the development of opportunistic taxa such as the gastropod Melanoides tuberculata. Decreases in taxonomic composition and community organisation between the upstream and downstream reaches of the river appear to be linked to less stable environmental conditions at the downstream sampling sites, and were compounded with a gradual increase in stress for organisms from the upper to lower reaches of the river. The composition, distribution and diversity characteristics of taxa collected is an indication that the ecological status of the Alibori River is under pressure, as a result of the agricultural activities along its banks