The Natural Park of Albufera (Valencia, Spain) is an important Mediterranean coastal wetland that suffers continuous environmental effects from human activities and water uses, mainly related to agriculture and urban/industrial sewage discharges. The aim of this research was to assess the water quality of the different aquatic environments of this wetland, taking into account the connection between them, the agricultural impact and the management of irrigation water. The UE Water Framework Directive was followed in order to evaluate the ecological and trophic status of water systems. Spatial approaches were used to integrate physicochemical data into GIS vector layers to map the more problematic points of pollution. The results showed a globally eutrophic system with poor ecological potential. The wetland is nutrient-overloaded during the entire rice cultivation period. Good-quality water inputs are deficient, since the river network already has high levels of nutrients and pollutants, especially in the northern area, where river water is mixed with inappropriate effluents from wastewater treatment plants. Agriculture and water management affected the area intensively up to the Albufera lake, modulating most of the studied variables. The information gathered here can help to optimize the global study and management of the coastal Mediterranean wetlands, which are highly linked to agriculture.