Nature-based solutions in lake restoration enable gradual ecosystem reconstruction without drastic and expensive intervention. Sustainable lake restoration involves limited external interference strong enough to initiate and maintain positive changes in the ecosystem. It was introduced in Lake Durowskie, an urban, flow-through lake situated in Western Poland, using hypolimnetic aeration, phosphorus precipitation with small doses of chemicals and biomanipulation in 2009, and is continued until today. Oxygen conditions in the lake hypolimnion after initial deterioration were gradually improved, and finally a shortening of the duration and range of oxygen deficits was observed. Nitrogen transformations were induced in the hypolimnion by water aeration as well, reducing ammonium N (30% during 2013–2017 in comparison to 2008) and increasing nitrates (90% in 2013–2017 in comparison to 2008). Phosphorus content was diminished (19% during 2015–2017 in relation to 2008 for SRP) due to effective iron-binding and a smaller amount of fresh organic matter being decomposed. Its reduction was related to lower phytoplankton biomass, expressed in a decrease of chlorophyll-a concentrations (55% reduction during 2013–2017 in comparison to 2008) and an increase in water transparency (two-fold during 2013–2017 in relation to 2008) throughout the nine years of treatment. A long-term restoration program, based on non-aggressive, multiple in-lake techniques was applied and, despite the lack of a reduction in total external loading, was able to suppress progressive eutrophication.