In deep stratified coastal lagoons, hypoxic waters that result from phytoplankton decomposition in the stratified bottom waters are often associated with eutrophication. Decomposing biomass reaches the bottom sediments and enriches them with nutrients and organic matter. Nutrients trapped in sediments are released with time and promote excessive phytoplankton growth in the surface water. Because eutrophication in lentic ecosystems progresses in a self-fuelling cycle, outflow is the only available process for exporting excess nutrients to recover from eutrophication. Thus, rehabilitation of eutrophic coastal lagoons that have limited seawater interactions is a long term process. The importance of nutrient release from sediments on eutrophication and the delay effect of internal nutrient loading on the rehabilitation of a eutrophic coastal lagoon with limited seawater exchange were analysed in this study. An ecological model that couples the water column and the sediment diagenesis processes, was developed for water quality management purposes. Our findings indicate that the recovery of the Lagoon from eutrophication will be taken decades even in the absence of external nutrient loading. Therefore, we suggest applying rehabilitation strategies that control the nutrient fluxes from sediments for a faster recovery from heavily eutrophic conditions. Land-based nutrient sources must also be controlled because they feed water column and the bottom sediments with nutrients. (C) 2017 International Research and Training Centre on Erosion and Sedimentation/the World Association for Sedimentation and Erosion Research. Published by Elsevier B.V. All rights reserved.