The significant contribution of phytoplankton to global primary production is regulated by several abiotic and biotic factors, which are often difficult to account for in natural systems. To address these challenges, we perturbed a summer plankton community from Narragansett Bay, Rhode Island, USA, by manipulating the temperature and nutrient conditions in a controlled short-term incubation experiment and tracked changes in phytoplankton community structure in response to fluctuations in phytoplankton physiology and microzooplankton grazing. Water was incubated at the in situ temperature (22°C) and at deviations from that temperature (± 4°C) with both macronutrient amendments (N, P, and Si addition) and unamended controls. We found nutrient availability and microzooplankton grazing to have pronounced and opposite impacts on phytoplankton size composition, with nutrient amendments shifting the phytoplankton community toward larger cells and grazing rates correlated with smaller phytoplankton communities and low-nutrient conditions. Nutrient amendments also altered cellular elemental ratios by increasing chlorophyll : C. Conversely, temperature was not found to have a direct impact on size or elemental stoichiometry, but did influence community composition. These findings paralleled prior observations from lab and field studies in Narragansett Bay which together suggest that over shorter timescales, nutrient availability may have a greater impact on phytoplankton community composition than temperature or grazing, altering phytoplankton nutritional value for higher trophic levels and as a result, secondary production. Thus, understanding underlying nutrient dynamics will be necessary to decipher how short-term changes in temperature or grazing may impact phytoplankton communities and the ecosystems they support.