Hydrological research in humid tropics is particularly challenging because of highly variable hydrological conditions and high socio-economic stresses caused by rapid population increase, as is the case of Nicaragua. The objective of this research is to understand the surface and subsurface runoff generation processes in a poorly gauged coastal catchment in Nicaragua under variable humid tropical conditions. Specifically, it focuses on identifying geomorphological and hydro-climatic controls on catchment response at different spatio-temporal scales and studies the link between hydrological processes and ecosystem conditions (i.e. mangrove forest). Catchment topography, geology and land use control surface and subsurface runoff generation. Spatio-temporal variability of precipitation affects availability of water resources, determines sources of surface runoff generation and induces changes in groundwater–surface interactions. Sustainable water resources management must prevent drastic alterations in catchment structural characteristics defined by forested areas and tidal sand ridges. Catchment response to hydro-climatic and geomorphologic controls supports the mangrove ecosystem freshwater needs. The outcome of this work is a contribution to the hydrological knowledge of poorly gauged catchment in humid tropics. It also provides scientific hydrological insights to support water resources management on the South Pacific coast of Nicaragua.