Transitional waters are ecosystems of important naturalistic value and enjoy different forms of protection. They are often subject to the threat of pollution phenomena due to anthropic activities and therefore objects of research for the choice of good monitoring, control and management practices. This study deals with the environmental analysis, conducted with water quality measurement campaigns and subsequent analysis of the data collected, of two lagoons in southern Italy, the Lesina lagoon and the Varano lagoon. These fall into the category of transitional waters sensu the Directive 2000/60/EC. The anthropic pressures and their impacts were evaluated in order to assess the environmental quality objectives stated by the mentioned European Directive. As a result, this study showed a non-critical state of the lagoons, but they will certainly be kept under observation.