Introduction. Manzherok Lake is the only habitat of the Red Book endemic water chestnut (Trapa pectinata) in the Altai Republic. In the second half of the 20th century, its catchment area underwent significant anthropogenic transformations, increasing the degradation of the lake ecosystem. To stabilize the state of the reservoir, in 2017–2018, its central part was cleared of the bottom silt (sapropels). Methods. In 2019–2020, as part of monitoring the state of the lake’s water area, 11 rounds of water testing were conducted at six points on two profiles. In total, we collected 72 water samples and studied their chemical composition and, partially, microbiological parameters. The suspended matter content, turbidity and oxidability of water were determined on an ongoing basis. Results. We identified a trend for a consistent decrease in the content of suspended particles and other indicators of the ecological state of water. The forecast for 2020 to improve the quality of lake water was confirmed. We also revealed other positive changes in the ecological state of Manzherok Lake after its clearing. Conclusion. We determined features of lake ecosystem self-restoration after rehabilitation and made a forecast regarding the preservation of positive trends in the restoration of water quality for the next 1–2 years. It is shown that the lake clearing of the bottom silt did not solve the problem of its rehabilitation to the full.