The impoundment of rivers by large dams is the biggest direct anthropogenic impact on the hydrological cycle. However, dams can help solving eutrophication in estuaries by controlling flow pulses, which in turn might enhance the advection of fish larval stages from their spawning and nursery areas. Thus, this work aimed to merge data on the abundance of anchovy eggs with MOHID hydrodynamic model for the Guadiana estuary, allowing dam/basin managers to set river discharge scenarios that might mitigate/prevent eutrophication, without compromising the presence of fish larval stages inside the estuary. Data on anchovy larval stages were assessed in the Guadiana estuary and adjacent coast and three simulation setups were developed. In Simulation A, anchovy eggs abundance was merged in the hydrodynamic model to compare the outputs with data on the abundance, distribution and development stage of anchovy eggs and larvae. In Simulation B, lagrangian particles were incorporated in the model to determine the percentage of particles released from the upper, middle and lower estuary that remain in the estuary along 10 days, in two tidal situations and in seven river discharge scenarios. In Simulation C, the abundance of anchovy eggs was merged in the model to select the discharge scenario(s) that do not compromise the presence of anchovy larval stages in the estuary. Results confirmed the spawning and nursery areas of anchovy and showed that scenarios B (Qmax = 20 m3 s−1) and C (Qmax = 50 m3 s−1) should be applied during neap tides. The choice between scenarios depends on the degree of eutrophication, the effectiveness of an inexistent monitoring program and on plankton response experiments to flushing and increased nutrient loading. This work produced an easy-to-use management tool for Guadiana managers, serving as an example to other estuarine sites around the world. Ultimately, this work suggests that river flow management must be guided by robust ecological studies, under an adequate sociological framework and adopting sustainable economic principles to maintain and improve the ecosystem services. Copyright © 2010 John Wiley & Sons, Ltd.