The Mondego estuary is a well-described system located on the North Atlantic Ocean, where cultural eutrophication progressed over the last decades of the 20th century. Consequently, and due to a large productivity of Ulva spp., Zostera noltii meadows were severely reduced with a concomitant decrease in environmental quality. In 1998, experimental mitigation measures were implemented, via changes in hydrology to increase circulation and diversion of nutrient-rich freshwater inflow, to reverse the process in the most affected area of the estuary e its South arm. The objective of this study was to assess the differences in response of primary producer assemblages to the implemented measures to reduce eutrophication. Results show that the mean concentrations of DIN suffered a notorious decrease due to a significant reduction in the ammonium concentra-tion in the water column, while DIP increased significantly. Primary producer assemblages showed different responses to these changes: phytoplankton, measured as concentration of chlorophyll a, did not show any significant changes; green macroalgae, mostly Ulva spp., suffered a large reduction in biomass, whereas Gracilaria gracilis and the macrophyte Zostera noltii biomasses increased greatly. Results show that phy-toplankton biomass has remained constant and suggest that the reduction in ammonium could have been responsible for the changes in the green macroalgal biomass. Light was the most likely factor in the response of seagrass whereas red macroalgal reaction seemed to be dependent on both light and ammonium.