Shallow lakes are highly vulnerable to damages caused by human activities and warming trends. To assess whether and how community structures of phytoplankton and nitrogen uptake respond to the combined effects of elevated temperature and eutrophication, we performed a mesocosm experiment in field by combining a 4.5 degrees C increase in temperature and the addition of phosphorus. Our results demonstrated that the combination of rising temperatures and phosphorus loading stimulated the maximum biomass built up by the phytoplankton community, and changed the phytoplankton community by significantly increasing the number of Chlorophyta and Cyanophyta, and decreasing that of Cryptophyta. We also examined the effects of climate warming and eutrophication on phytoplankton nitrogen uptake and dynamics using N-15 tracer techniques. The addition of phosphorus slightly increased the phytoplankton nitrate uptake velocity and relative preference index, but decreased the nitrate uptake turnover time. Warming relatively increased the ammonium uptake velocity and the relative preference index, but decreased the ammonium turnover time. In kinetic studies, NH4+ exhibited a higher maximum uptake rate (V-max) and a lower half-saturation constant (K-s) than NO3- substrates due to temperature elevation and the addition of phosphorus. Hence, warming and eutrophication increased the capacity of phytoplankton for NH4+ uptake and their affinity at low substrate concentrations. Thus, the combined effects of climate warming and phosphorus nutrient availability may increase the prevalence of Chlorophyta and Cyanophyta, and change the nitrogen cycling of aquatic ecosystems.