Summary1. High water column NO3− concentrations, low light availability and anoxic, muddy sediments are hypothesised to be key factors hampering growth of rooted submerged plants in shallow, eutrophic fresh water systems. In this study, the relative roles and interacting effects of these potential stressors on survival, growth, allocation of biomass and foliar nutrient concentrations of Potamogeton alpinus were determined in a mesocosm experiment using contrasting values of each factor (500 versus 0 μmol L−1 NO3−; low irradiance, corresponding to the eutrophic environment, versus ambient irradiance; and muddy versus sandy sediment).2. Low irradiance, high NO3− and sandy sediment led to reduced growth. In a muddy sediment, plants had lower root : shoot ratios than in a sandy sediment.3. Growth at high NO3− and on the sandy sediment resulted in lower foliar N and C concentrations than in the contrasting treatments. The C : N ratio was higher at high NO3− and on the sandy sediment. Foliar P was higher on the muddy than on the sandy sediment but was not affected by irradiance or NO3−. The N : P ratio was lowest at high NO3− on the sandy sediment.4. Total foliar free amino acid concentration was lowest on sand, low irradiance and high NO3−. Total free amino acid concentration and growth were not correlated.5. Turbidity and ortho‐PO43− concentration of the water layer were lower at high water column NO3− indicating that the growth reduction was not associated with increased algal growth but that physiological mechanisms were involved.6. We conclude that high water column NO3− concentrations can significantly reduce the growth of ammonium preferring rooted submerged species such as P. alpinus, particularly on sediments with a relatively low nutrient availability. Further experiments are needed to assess potential negative effects on other species and to further elucidate the underlying physiological mechanisms.