This study aimed to determine whether and how the disruption of river flow, during the filling of the Alqueva dam, influenced the variability of abiotic and biotic factors in the Guadiana estuary, particularly the abundance and distribution of anchovy eggs. River inflow was found to be the most important factor in determining abiotic and biotic variability in the Guadiana estuary. Seasonal patterns were obscured by long periods of low inflow (mid April to early December 2002), which caused marked changes in the estuary. The estuarine turbidity maximum zone was displaced towards the upper estuary, to at least 38 km from the river mouth, 8 to 16 km upstream from previous records. The dynamics of nutrient stoichiometry was also affected. In the upper and middle estuary, P was more potential limiting than N and potential Si limitation was only frequent on the coast, with direct and/or indirect influence in changing phytoplankton dynamics and composition. Previously, the upper estuary alternated between potential P limitation during winter, Si limitation during spring and mid summer and N limitation during mid summer and autumn. The flooding of vast areas in the catchment of the dam probably caused the increase of DSi concentrations, as well as maximal N and P loadings. The abundance of larval stages of anchovy decreased, putatively because estuarine productivity has also decreased. In April 2002 there was an uncontrolled discharge from the Alqueva dam, which reduced the abundance of anchovy eggs by 99.99%. It is suggested that dam managers should mimic, as much as possible, the natural river flow, in order to minimize the impact on downstream ecosystems. Management efforts should not be restricted to the areas upstream of the dam, but should also encompass the estuary and adjacent coastal area.