Abstract. – The characteristic high variability and low predictability of coastal lagoons, due to strong changes in marine and freshwater inputs, make these ecosystems an interesting casestudy. The small Melides landlocked coastal lagoon in SW Portugal is a paradigmatic example, with a biological community highly stressed by these phenomena. Benthic macroinvertebrate samples were collected in 1998/99 and 2009 and each year, in different seasons and addressing different environmental conditions influenced by the connection to the sea and rainfall regime. Major spatial and temporal patterns in benthic communities were investigated using some invertebrate attributes (e.g. community composition, density, species richness and diversity). A very low taxonomic species richness and diversity was found in the Melides lagoon and only a much reduced number of species occurred along all sampling periods and in both sampling campaigns. Although the colonization events play a crucial role, the persistence of the observed species was mainly associated to abiotic factors, such as salinity, temperature and dissolved oxygen. Despite the potential reduction in anthropogenic pressure, by the construction of a sewage treatment plant and a reduction of urban occupation, the ecological status did not improve and the high level of natural environmental variably in the lagoon seems to be the dominant stressor influencing benthic invertebrate communities.