Eutrophication of two urban temperate dimictic lakes in Berlin (Germany), smaller Schlachtensee (0.4 km2) and larger Lake Tegel (3 km2), caused total phosphorus (TP) concentrations up to 800 μg/L and a complete loss of their diverse submerged vegetation in the 1960s due to poor light conditions. Phosphorus stripping of their inflow began in the 1980s and caused a pronounced decline of their epilimnetic TP concentrations, eventually leading to reduced phytoplankton biomass and turbidity. Despite increased light availability, recovery of abundance as well as species diversity of submerged macrophytes was delayed by more than a decade, especially in the smaller lake. Slow oxidization of sapropelic sediment unsuitable for macrophyte growth, periphyton shading, herbivory, and/or lack of a viable seed bank were potential hampering factors. The present submerged vegetation, however, may already support mechanisms positively influencing water transparency such as providing habitat to enhance the ratio of piscivorous to planktivorous fish. Characeae meadows, typical for both lakes during their former mesotrophic state, so far only reoccurred in smaller Schlachtensee. Neither species composition nor abundance reversed back to the macrophyte community present in the nineteenth century. Although TP concentrations may decline further and some rare species have been detected, reassembly of this plant community will most probably not occur because many submerged macrophyte species have become rare throughout northwest Europe.