The supply of allochthonous organic matter with river water to the lakes rises in the new climatic conditions of Karelia (mild winters, an increase in the amount of liquid precipitation, less freezing of the soil). In connection with the geochemical peculiarities of Fennoscandia, more quantity of humic substances in a complex with iron and phosphorus enter the water bodies. These processes can lead to a change in the hydrochemical regime, water quality and habitat of the biota. For the first time for lakes of Karelia, long-term changes (1963–2017) of parameters, which are markers of allochthonous organic matter, were estimated on the example of Petrozavodsk Bay of Onego Lake. It was found that since the 1990s, the following characteristics significantly increase in Petrozavodsk Bay water: the color of water (from 56 to 73 degrees), the content of suspended matter (from 1.6 to 3 mg/l), iron (from 0.12 to 0.42 mg/l), phosphorus (from 12 to 22 μg/l). This leads to changes in the carbonate system of the bay water. The concentration of carbon dioxide increases significantly (from 1.2 to 3.0 mg/l), the pH value drops (from 7.22 to 7.12) and the oxygen content diminishes (from 101 to 92% of saturation). The Spearman correlation coefficients between the chemical characteristics and the year of study were the highest for the spring period, when the bay is separated from the open part of the lake by thermal bar and is strongly influenced by river water. Simultaneously with the change in the hydrochemical regime, there is an increase in the amount of iron in the upper layer of silts (from 0.65 to 4.8% of the air-dry sample). This led to a decrease in the number of macrozoobenthos 6–7 times.