Small lakes of the boreal zone are highly sensitive indicators of both global environmental change and local anthropogenic pressure. This work presents the results of multidisciplinary study of three small, seasonally stratified lakes of NW Russia, conducted since 2002 to the present time. These lakes were subjected to various degree of impact by rural population and agricultural activity since the beginning of twentieth century but the population and anthropogenic pressure have decreased since 1990s. To monitor the recovering of these lakes from human impact and to relate the evolution of their hydrochemical parameters to short-term weather events and global climatic trend, we measured the lake water temperature and chemical composition (carbon, macro- and micronutrients, trace elements) in summer and winter over full depth of the water column. The pH and concentration of DIC, SO4 and H2S decreased over past decade. Concentrations of Si and nitrite increased over past 15 years, probably linked to progressive replacement of diatoms by cyanobacteria. We also recorded an increase in concentration of Cl and major cations in all lakes, likely linked to increasing connection to groundwater reservoirs. Some trace elements (Fe, Mn, Al, Zn, As, Pb) can serve as suitable indicators of on-going natural processes controlling lake response to external factors. Unlike widely reported global trend of DOC and Fe concentration increase in boreal surface waters of Europe and Northern America, such trend was not discernable in studied Fe-rich humic lakes. We conclude on the necessity of complex, multidisciplinary studies of small humic lakes in the boreal zone, because these “model” lakes can serve as important proxies of on-going environmental changes in highly abundant aquatic ecosystems of poorly characterized regions of NW Russia.