Direct and indirect anthropopressure on water ecosystems is the serious problem throughout the world.. In the Northern Hemisphere, an increase in average air temperatures is observed, which implies the occurrence of a shorter period of snow and ice cover during the winter season. The winter 2019/2020 was unusual, because that was the first time in the record, that a complete lack of permanent ice cover was observed on numerous lakes in Poland. Such unusual conditions could influence lake functioning. Hence we analyzed the chemistry of the water–sediment interface (near-bottom and interstitial water and sediment) in the shallow, eutrophic Mielenko Lake (area 7.9 ha, max depth 1.9 m) in 2013 and 2019–2022 period to assess the influence of prolonged water circulation on the bottom zone. Mielenko Lake was subjected to a phosphorus inactivation procedure using Al and Fe salts (PAX 18, PIX 111) in 2020 and 2021. Our research revealed that unusually prolonged winter circulation caused a significant decrease in organic matter content in bottom sediment in 2020, as well as a decrease in NaOH-nrP fraction and TP amounts. That effect was short-term and it did not significantly influence the NaOH-rP fraction amounts. The released P was probably built in macrophytes biomass during vegetation season, because P inactivation has been limiting phytoplankton proliferation, and it favored shifting to a clearwater state with macrophytes domination. This was confirmed by decreasing in phytoplankton biomass, and a massive expansion of the macrophytes range noted in the second year of restoration. Our study shows, that P inactivation could mitigate the negative effects of warm winters in shallow lakes.