The coastal zone of Yucatan Peninsula has been recognized as the most important environment to the economic development of this region. Different projects have been conducted in this area, including harbors, tourist, commercial, and aquaculture infrastructure, among others. However, there is no information available on what are ''normal'' concentrations of dissolved inorganic nutrients (DIN) and chlorophyll-a (Chl-a) for these regions. In order to establish the base-lines of selected water quality parameters four coastal areas of the north of Yucatan Peninsula (SE, Mexico) a monitoring program has been conducted since 1999 in four localities of the north of Yucatan which show differences on the kind and intensity of anthropogenic impacts. The results show that Dzilam is the site with the best water quality conditions and a conservation program must be implemented, while Sisal and Progreso are the ports with the worst water quality and where different strategies must be implemented, such as water management of the shrimp farm effluents through constructed wetlands in Sisal, or water waste treatment and facilitation of water circulation in the Progreso port. Other results from phytoplankton community and submerged aquatic vegetation indicate that these components must be incorporated into water quality programs in order to effectively identify the problems and monitor the success of management strategies. These results can be used to understand the linkages between stressors from the activities and