Eutrophication has a profound impact on ecosystems worldwide. Grass carp Ctenopharyngodon idella, an herbivorous fish, has been introduced to control aquatic plant overgrowth caused by eutrophication, but could have other, potentially detrimental, effects. We used the Po di Volano basin (south of the Po River delta, northern Italy) as a test case to explore whether grass carp effects on canal aquatic vegetation could be at the root of historical changes in N loads exported from the basin to the Goro Lagoon. We modeled the aquatic vegetation production and standing crop, its denitrification potential, and its consumption by introduced grass carp. We then examined whether changes in historical nitrogen loads matched the modeled losses of the drainage network denitrification function or other changes in agricultural practices. Our results indicate that introduced grass carp could completely remove submerged vegetation in the Po di Volano canal network, which could – in turn – lead to substantial loss of the denitrification function of the system, causing in an increase in downstream nitrogen loads. A corresponding increase, matching both timing and magnitude, was detected in historical nitrogen loads to the Goro Lagoon, which were significantly different before and after the time of modeled collapse of the denitrification function. This increase was not clearly linked to watershed use or agricultural practices, which implies that the loss of the denitrification function through grass carp overgrazing could be a likely explanation of the increase in downstream nitrogen loads. Perhaps for the first time, we provide evidence that a freshwater fish introduction could have caused long-lasting changes in nutrient dynamics that are exported downstream to areas where the fish is not present.