Temporary ponds represent a specific type of ecosystem extensively widespread worldwide. They are better known as copular pools, ephemeral waters, karst sinkholes, seasonal wetlands, and vernal pools. Among these, Mediterranean Temporary Ponds (MTPs) represent a priority habitat according to the Natura 2000 network of the European Union. Their main characteristic is represented by their depth of only a few centimeters and lack of communication with permanent water bodies. MTPs habitats are vulnerable to human activities, especially agriculture, and they are considered priority habitats to safeguard. Threats affecting this habitat are various and many and depend on specific site conditions, including intensive agriculture, tree planting, abandonment of traditional land use, and excessive grazing. In the present manuscript, we report the results of monitoring activity of some of these sites in Southern Italy aimed at understanding the ecological status of these ephemeral ecosystems with a specially developed methodology based on data integration.