Long term macrobenthos data together with physical habitat parameters were analysed to investigate spatial and temporal changes at an estuary under different anthropogenic pressures, mainly increasing shellfish farming. The aim was to assess the possible impacts of these pressures on the macrobenthic communities by comparing a period before and after changes in these pressures. Benthic samples were seasonally collected in 1990 (before major anthropogenic changes), 2000 and 2005 at the same sampling stations located on three different habitats in the Eo estuary (Northern Spanish coast). Multivariate and univariate methods were used to assess spatial variability of benthic assemblages and to compare community changes over time. Data from 1990 was assumed as the reference situation to appraise the subsequent impacts. We observed a significant spatial variability of the benthic assemblages in the system as a function of habitat heterogeneity in relation to sediment composition, presence/absence and density of seagrasses, and hydrodynamic regime. Changes were detected in the community composition at all sites during this 15 year period. The extent of changes was related to initial community conditions, rather than the intensity of the pressure. The results suggest that the responses of the benthic communities to human induced perturbations occurring in the system are largely dependent on its intrinsic buffer capacity, and that these communities have been able to cope with an increasing environmental stress (organic enrichment). In conclusion, to keep shellfish farming at a sustainable level without undesirable impacts, the disturbance intensity must be kept below the system carrying capacity. This will allow natural communities to cope with pressures and thus avoid further deterioration in ecological quality.