Lake Onego is the second largest freshwater lake in Europe experiencing a multifactorial impact. The environmental pressures on the lake ecosystem has changed over the last decade because of the intensive development of aquaculture, reduction of wastewater discharges, internal load, and population redistribution. The purpose of this study was to assess whether these changes have affected the water quality of Lake Onego and to assess their extent. Data collected in 2019–2021 were used to indicate distribution and spatial heterogeneity in the chemical composition of lake water. The following parameters were considered: pH, conductivity, total suspended solids (TSS), Na+, Cl-, nutrients (P-PO4, TP, N-NH4, N-NO3, TN), organic matter (OM) (TOC, lignosulfonates, BOD5, CODMn, CODCr, color), Fe, Mn, and heavy metals (Cu, Ni, Zn, Cd, Pb). Data collected earlier (1992–2018) were used to indicate temporary changes in nutrients and OM concentrations. The largest tributaries deliver nutrients, TSS, and OM associated with Fe, Mn, and Cu to the lake water. Water contamination was observed in the Petrozavodsk and Kondopoga Bays experiencing anthropogenic load from domestic and Pulp and Paper Mill wastewaters accordingly, which is mainly evidenced by increased concentrations of OM and nutrients. The water quality in the Petrozavodsk Bay is significantly deteriorated in winter and spring due to the Shuya River discharge, which caused an increase in TP and OM concentration in the bay in the last three decades. Gradual increase in TP and OM content since 1992 also been observed in the central part of the Kondopoga Bay, which was mainly caused by the trout farm impact. At the same time, oligotrophication was observed in the Povenets Bay. The main waterbody of the lake still preserves its high water quality; however, the tendency for its eutrophication is evident by the decrease of the rate of mineral nitrogen to total phosphorus.