Benthic faunal activity and density play an important role in determining the rates of benthic nutrient fluxes, which enrich the water column and contribute to phytoplankton growth. The intensity of nutrient fluxes in the Bay of Brest depends on the density of the invasive gastropod, Crepidula fornicata. In order to study the impact of benthic fluxes on phytoplankton dynamics, realistic daily nutrient inputs simulating various densities of C. fornicata were added to six enclosures during three weeks. The increase in fertilization intensity influenced the phytoplankton biomass. A succession from Chaetoceros spp. to Pseudo-nitzschia spp. and Leptocylindrus danicus was observed in all enclosures, but the dynamics of successions were different. Pseudo-nitzschia spp. was favored in the three more fertilized enclosures, while Chaetoceros spp. persisted longer in less enriched enclosures. Despite an apparent nitrogen limitation, the quantum efficiency of PSII (Fv/Fm) was high (>0.5) and stable in all enclosures. The maximal photosynthetic capacity (PBmax) was also invariable and oscillated around an average value of 2.23 mg C (mg Chl a)−1 h−1. The stability of Fv/Fm and PBmax observed at different nutrient input intensities demonstrates that the daily inputs maintained the physiological balance of the microalgae. The maximal light utilization efficiency (α) and the light saturation parameter (Ek) were also quite stable after day 8, which reveals that photosynthetic parameters were driven by growth constraints due to nutrient availability and not by incident light or species successions. We suggest that our results correspond to an "Ek independent variation" regulation. We propose that such regulation of photosynthetic parameters appears when there are frequent nutrient additions which do not allow replete nutrient conditions to be reached but lead to physiological equilibrium. Thanks to our results we can understand how even low benthic fluxes, by supporting their cellular physiological status, allowed diatoms to dominate the phytoplankton community in the six enclosures. These results confirm the importance of daily benthic inputs as much as the amount of nutrient inputs. However, we suggest that high benthic fluxes have a buffering effect on nutrient availability, thereby limiting the consequences of short-term events which can entail a sudden increase of nutrient input, and are known to promote Dinophyta bloom formation.