Despite there are multiple causes and consequences of eutrophication, this article analyses key aspects in the current context of Uruguay, emphasizing on cyanobacterial blooms as one of the most frequent and noticeable consequences. The worsening of eutrophication and its symptoms predicted with climate change, the keys for the reduction of diffuse losses of phosphorus with surface runoff on agricultural lands and the ongoing and future changes of water governance and management of the problem are some of the most important issues considered here. In this analysis, we also identify several challenges, both to fill knowledge gaps and in the arena of environmental management.