Effect of global change variables on the structure and photosynthesis of phytoplankton communities was evaluated in three different sites of the Patagonian coast of Argentina: enclosed bay (Puerto Madryn, PM), estuarine (Playa Unión, PU), and open waters (Isla Escondida, IE). We exposed samples to two contrasting scenarios: Present (nutrients at in situ levels) vs. Future (with lowered pH and higher nutrients inputs), and determined growth and photosynthetic responses after 2 days of acclimation. Under the Future condition phytoplankton growth was higher in the estuarine site compared to those in PM and IE. This effect was the most pronounced on large diatoms. While the increase of photosynthetic activity was not always observed in the Future scenario, the lower photosynthetic electron requirement for carbon fixation (Φe,C = ETR/PmB) in this scenario compared to the Present, suggests a more effective energy utilization. Long-term experiments were also conducted to assess the responses along a 4 days acclimation period in PU. Diatoms benefited from the Future conditions and had significantly higher growth rates than in the Present. In addition, Φe,C was lower after the acclimation period in the Future scenario, compared to the Present. Our results suggest that the availability, frequency and amount of nutrients play a key role when evaluating the effects of global change on natural phytoplankton communities. The observed changes in diatom growth under the Future scenario in PU and IE and photosynthesis may have implications in the local trophodynamics by bottom up control.