Coastal lagoons are productive and highly vulnerable ecosystems, but their management is still problematic mostly because they constitute transitional interface between terrestrial and marine domains. The “4th European Conference on Coastal Lagoon Research – Research and Management for the conservation of coastal lagoon ecosystems, South North comparisons”, was focused on the scientific research on coastal lagoons and the management for their conservation and sustainable use. Selected contributions were considered in this special issue of Estuarine Coastal and Shelf Science “Research and Management for the conservation of coastal lagoon ecosystems” as they deal with three important aspects for coastal lagoons management: (1) the design of monitoring programmes using biological compartments, (2) the ecosystem functioning and the impacts of perturbations and (3) ecosystem trajectories particularly after ecosystem restoration. Here we introduce the selected papers published in this issue, place these contributions in the perspective of the science-management interface and discuss new issues for coastal lagoon management.