Sustainable restoration of eutrophic lakes remains a vital challenge, with probiotic bioremediation providing a non-invasive alternative to conventional chemical approaches. This study assesses the effectiveness of Effective Microorganisms (EM) technology in restoring Lake Jeziorko (Poland), using water mites (Hydrachnidia) as sensitive bioindicators of habitat change. During the monitoring period lasting a total of 35 months (samples were taken each time in July for three years) across littoral and profundal zones, collecting 9,739 water mite individuals from 38 species. Bathymetric analysis confirmed a decrease in bottom sediment thickness, which probably triggered a clear response in benthic fauna. Although the initial year showed a lake-wide increase in species richness, long-term trends reveal a split: littoral communities declined due to external nutrient inputs and cyanobacterial blooms, while profundal communities (dominated by typical lake taxa such as Neumania limosa and Piona stjordalensis) remained stable and showed signs of improved sediment oxygenation. These findings indicate that while probiotic bioremediation effectively conditions deep-water habitats and reduces sediment volume, it is not sufficient alone to counter external eutrophication pressures. Additionally, these studies indicate that profundal aquatic mite communities show a clear improvement in profundal conditions, while littoral water mites indicate that the ecological situation did not improve permanently.