The article presents the results of coupled palynological and geochemical studies of five various genesis lakes, located along the route of the expedition “In the footsteps of Alexander von Humboldt in Siberia, Altai and Eastern Kazakhstan”, dedicated to the double anniversary: the 190th anniversary of the expedition across Russia of the famous scientist and his 250th birthday. A geochemical analysis of water and bottom sediments of Ik Lake (Siberia), Lakes Kolyvanskoe and Beloe (Altai), Lake Bezymyannoe (Kazakhstan) and Nagornyi Pond (Altai) was carried out. Based on their results an assessment of studied lakes ecological state was given through single and integral criteria. A high level of pollution was noted for Nagornyi Pond and Lake Bezymyannoe, which is caused by a significant technogenic load from nearby mines. This is consistent with the data of palynological research. The aquatic ecosystems of Lakes Kolyvanskoe and Beloe are characterized by a satisfactory ecological situation, but they experience an increased recreational load. The results of spore-pollen analysis and analysis of non-pollen palynomorphs showed the low ability of these lakes to self-healing. The most favorable ecological state and high self-cleaning capacity were noted for Lake Ik, which is consistent with the data of palynological studies. It is being confirmed with the results of palynological studies. It was therefore concluded about the ability to make a quick assessment of the aquatic ecosystems’ ecological state by studying lakes using coupled palynological and geochemical analysis.