Summary1. Fish community structure and habitat distribution of the abundant species roach, perch and ruffe were studied in Lake Nordborg (Denmark) before (August 2006) and after (August 2007) aluminium treatment to reduce internal phosphorus loading.2. Rapid changes in fish community structure, abundance and habitat distribution occurred following a decline in in‐lake phosphorus concentrations from 280 to 37 μg P L−1 and an increase in Secchi depth transparency from 1.1 to 1.9 m (August). The proportion of perch in overnight gill net catches increased, whilst roach decreased, and the average weight of all key species increased.3. The habitat distribution of perch and roach changed from a high proportion in the upper pelagic and littoral zones in 2006, towards enhanced proportions in the deeper pelagic and profundal zone in 2007. The abundance of large‐bodied zooplankton increased and the abundance of benthic invertebrates decreased in the same period, suggesting that the habitat shift was not induced by food limitation.4. Ruffe shifted from the littoral and upper profundal zones towards the deep profundal zone, likely reflecting an increased predation risk in the littoral zone and better oxygen conditions in the deep profundal.5. Our results indicate that enhanced risk of predation in the upper pelagic and the littoral zones and perhaps improved oxygen concentrations in the deeper profundal zone at decreasing turbidity are responsible for the observed habitat shift. The results indicate that fish respond rapidly to changes in nutrient state, both in terms of community structure and habitat use.