We integrate information on functional diversity (FD) patterns from estuarine intertidal benthic communities from different habitats and along a temporal disturbance gradient, to understand the drivers of species coexistence patterns. Species and traits' biomass levels seemed to be first determined by habitat filtering, selecting those traits better adapted to the biologically challenging estuarine environment. Within that subset of traits and within each habitat, biotic interactions were probably high, as evidenced by high α-diversity and community weighted mean differences. The former patterns hold for the disturbance/recovery scenario considered. However, as the estuary recovered, biomass became more distributed among different trait categories, consistent with increases in FD when the seagrass started to increase. Policy towards the restoration of seagrass bed and other biogenic structures, and improving the connectivity within adjacent systems were confirmed and suggested, as this would imply higher FD and potentially higher resilience to disturbance within the estuarine intertidal system.