The purpose of this research was to assess the effects of dredging performed in a marginal wetland colonized by aquatic macrophytes on eutrophication of the adjacent shallow tropical lake (Imboassica Lake, Brazil). The river mouth of the Imboassica River that drains into Imboassica Lake had been densely colonized by aquatic vegetation dominated by Typha domingensis (Pers.) when it was dredged. Total and dissolved nitrogen and phosphorus concentrations were measured monthly over 13 years at four stations in the Imboassica river-lake system. Dredging activities reduced phosphorus and nitrogen retention at the river mouth and subsequently increased these nutrient stocks in the lake waters. Nutrient retention by non-dredged wetland was estimated to be ca. 1,200 kg year⁻¹ (87.3 g m⁻² year⁻¹) for nitrogen and 60 kg year⁻¹ (4.5 g m⁻² year⁻¹) for phosphorus. Our whole-lake approach suggested that dredging might intensify rather than mitigate eutrophication in shallow tropical lakes when the removal of aquatic macrophytes is coupled to the persistence of anthropogenic nutrient inputs from the watershed.