The Mondego estuary, a shallow warm-temperate intertidal system located on the west coast of Portugal, has for some decades been under severe ecological stress, mainly caused by eutrophication. Water circulation in this system was, until 1998, mainly dependent on tides and on the freshwater input of a small tributary artificially controlled by a sluice. After 1998, the sluice opening was effectively minimised to reduce the nutrient loading, and the system hydrodynamics improved due to engineering work in the upstream areas. The objective of the present study was to evaluate the effect of the mitigation measures implemented in 1998. Changes to the hydrodynamics of the system were assessed using precipitation and salinity data in relation to the concentrations of dissolved inorganic nutrients, as well as the linkage between dissolved N:P ratios and the biological parameters (phytoplankton chlorophyll a concentrations, green macroalgal biomass and seagrass biomass). Two distinctive periods were compared, over a ten year period: from January 1993 to January 1997 and from January 1999 until January 2003. The effective reduction in the dissolved N:P atomic ratio from 37.7 to 13.2 after 1998 is a result of lowered ammonia, but not the oxidised forms of nitrogen (nitrate plus nitrite), or increased concentrations of dissolved inorganic phosphorus. Results suggest that the phytoplankton is not nutrient limited, yet maximum and mean biomass of green macroalgae was reduced by one order of magnitude after the mitigation measures. This suggests that besides lowering the water residence time of the system, macroalgal growth became nitrogen limited. In parallel to these changes the seagrass-covered area and biomass of Zostera noltii showed signs of recovery ; http://dx.doi.org/10.1016/j.ecss.2005.07.009