Lake Konin is a small and shallow lake under the influence of highly eutrophic riverine waters. Feeding the lake as a backwater during high water level periods, the River Obra had exerted a decisive impact on lake water quality, and thus a new dike with a closing device was created. Protective measures were followed by the application of Effective Microorganisms (EM), aiming at a reduction in nutrient concentrations and CyanoHABs. Positive changes in the ecosystem were initiated (increased phytoplankton diversity), but cyanobacteria blooms were still present due to high nutrient content. Some changes were observed in the lake sediments (phosphorus (P) and its fractions, P in pore waters, organic matter and experimental assessment of internal P loading) studied before and during treatment. A slight increase in P content in sediments was noted, as a result of an increase in the Res-P fraction. Simultaneously, a decrease in the most mobile fractions was observed. Summer internal P load was reduced from 5.4 kgP d−1 before the treatment to less than 1 kgP d−1 in the first year, but increased again in the second year to 4.5 kgP d−1. Similarly to lake water quality, positive changes were induced in the lake sediments; nevertheless, they still acted as an important source of nutrients for primary producers. Additional restoration methods shall be considered, as combined treatments used simultaneously are reported to be the most effective for water quality improvement.