A 1-D ecohydrology model is proposed that integrates physical, chemical and biological processes in the Guadiana Estuary during low flow conditions and that predicts the ecosystem health as determined by the following variables: river discharge, nutrients, suspended particulate matter, phytoplankton, zooplankton, bivalves, zooplanktivorous fish and carnivorous/omnivorous fish. Low flow conditions prevail now that the Alqueva dam has been constructed. The ecological sub-model is based on the non-linear Lotka-Volterra equation. The model is successful in capturing the observations of along-river changes in these variables. Keywords: ecohydrology, marine ecology, flushing, modelling, dam, flow regulation, Portugal, Alqueva dam, Guadiana Estuary.