The Pietra del Pertusillo freshwater reservoir is a major artificial lake of environmental, biological, and ecological importance located in the Basilicata region, southern Italy. The reservoir arch-gravity dam was completed in 1963 for producing hydroelectric energy and providing water for human use, and nearby there are potential sources of anthropogenic pollution such as urban and industrial activities. For the first time, the minero-chemistry of the lake and fluvio-lacustrine sediments of the reservoir have been evaluated to assess the environmental quality. Moreover, the composition of fluvial sediments derived from the peri-lacual zone of the reservoir and of local outcropping bedrock were also studied to understand the factors affecting the behavior of elements in the freshwater reservoir, with particular attention paid to heavy metals. In Italy, specific regulatory values concerning the element threshold concentration for lake and river sediments do not exist, and for this reason, soil threshold values are considered the standard for sediments of internal waters. The evaluation of the environmental quality of reservoir sediments has been performed using enrichment factors obtained with respect to the average composition of a reconstructed local upper continental crust. We suggest this method as an innovative standard in similar conditions worldwide. In the studied reservoir sediments, the trace elements that may be of some environmental concern are Cr, Cu, Zn, As, and Pb although, at this stage, the distribution of these elements appears to be mostly driven by geogenic processes. However, within the frame of the assessment and the preservation of the quality of aquatic environments, particular attention has to be paid to As (which shows median value of 10 ppm, reaching a maximum value of 26 ppm in Quaternary sediments), constantly enriched in the lacustrine samples and especially in the fine-grained fraction (median = 8.5 ppm).