The River Merse basin is situated between the provinces of Siena and Grosseto. During the last few centuries, it has been subjected to intense mining operations. Being polluted because of this mining activity since the times of Industrial Revolution, the river has recently received renewed media coverage that has led to a process of decontamination, ended in 2009. According to the studies on the environmental quality run by the ARPAT between 2011 and 2012, the result of the decontamination has been only partially successful, as the environmental quality of the river ranges from “moderately deteriorated” to “deeply deteriorated”. In this study, we carried out an analysis of the environmental quality of the hydrographic system of the Merse river in five transects falling in the tract between the municipalities Montieri and Pari.