The southwestern coast of India is drained by many small rivers with lengths less than 250 km and catchment areas less than 6,500 km(2). These rivers are perennial and are also the major drinking water sources in the region. But, the fast pace of urbanization, industrialization, fertilizer intensive agricultural activities and rise in pilgrim tourism in the past four to five decades have imposed marked changes in water quality and solute fluxes of many of these rivers. The problems have aggravated further due to leaching of ionic constituents from the organic-rich (peaty) impervious sub-surface layers that are exposed due to channel incision resulting from indiscriminate instream mining for construction-grade sand and gravel. In this context, an attempt has been made here to evaluate the water quality and the net nutrient flux of one of the important rivers in the southwestern coast of India, the Manimala river which has a length of about 90 km and catchment area of 847 km(2). The river exhibits seasonal variation in most of the water quality parameters (pH, electrical conductivity, dissolved oxygen, total dissolved solids, Ca, Mg, Na, K, Fe, HCO(3), NO(2)-N, NO(3)-N, P[Formula: see text], P[Formula: see text], chloride, SO(4), and SiO(2)). Except for NO(3)-N and SiO(2), all the other parameters are generally enriched in non-monsoon (December-May) samples than that of monsoon (June-November). The flux estimation reveals that the Manimala river transports an amount of 2,308 t y(-1) of dissolved inorganic nitrogen, 87 t y(-1) dissolved inorganic phosphorus, and 9246 t y(-1) of SO(4), and 1984 t y(-1) K into the receiving coastal waters. These together constitute about 23% of the total dissolved fluxes transported by the Manimala river. Based on the study, a set of mitigation measures are also suggested to improve the overall water quality of small catchment rivers of the densely populated tropics in general and the south western coast in particular.