As in many countries worldwide, deterioration of quality of water in Morocco’s natural reserves continues, such that an inventory of qualities of these reserves has become necessary. Based on statistical analyses of the data collected by measuring nineteen physicochemical variables, and applying an index, the comprehensive pollution index, to those data, the quality of the waters of Lake Dayat Roumi, Morocco, were assessed. Waters of the lake are currently characterized by a salinity of 921.7 mg Cl−/L and 124.2 mg sulfates/L. The concentration of chloride exceeds the value indicated in the standard norms. This can affect the composition of the sediment, overlying water, and specific composition of biota in the lake. Status and trends of values of other parameters also indicate deterioration of water quality in this lake. Multivariate statistical analysis made it possible to differentiate four clusters of samples according to their physicochemical characteristics. These groups are due to inputs from three sources of materials: leaching of rocks from the watershed and plantations, discharge of domestic wastewater and runoff water. Samples taken from deeper parts of the lake indicate a depression of concentrations of dissolved oxygen during the hot season. The analysis results demonstrate the heterogeneous degradation of the water quality in the peripheral areas and deep parts of the lake, favored by the leaching of soils by rainwater, which, when sufficiently severe, can cause repeated mortalities of fishes. This situation requires regular water quality monitoring to develop a management plan for restoration of water quality in the lake to preserve valued ecological services.