Ecological status classification systems based on biological elements (e.g., macroinvertebrate communities) are dependent on their response to different pressures. However, there is a need to determine if invasive species should be incorporated to indicator parameters (i.e. metrics based on measurements of richness and diversity) or as a pressure affecting such parameters. Moreover, because ecosystem classification systems are lacking for northwestern Iberian estuaries, there is even the possibility to develop a new metric penalizing presence or abundance of invasive species. To increase our understanding on this topic, we analyze the taxonomic and functional responses of benthic macroinvertebrates to Corbicula invasion along the environmental gradient of 12 northwestern Iberian estuaries. Macroinvertebrate assemblages were described and compared between invaded and uninvaded sections. Additionally, to assess differences in community structure, macroinvertebrate assemblages’ similarity was examined between two distinct estuarine sections (freshwater and oligohaline vs transitional water and mesohaline) and among water body types, including and excluding Corbicula from the analysis. The salinity gradient was the main driver explaining changes in macroinvertebrate assemblages and in functional group distribution. Freshwater and transitional water sections clearly differed in macroinvertebrate assemblages and functional groups composition. In addition, differences among river types in macroinvertebrate composition were found. Corbicula inclusion or exclusion from multivariate community analysis significantly affected the results in functional feeding group composition in the Cantabric-Atlantic siliceous river axis type. Nevertheless, considering Corbicula as a pressure at the regional scale did not provide different results in diversity indices calculation. Hence, we argue that because Corbicula eradication is virtually impossible, it should be included as an additional metric evidencing its presence as a negative indication, or be included within other indicator metrics used in the assessment of the ecological status, for instance in invertebrate abundance metrics were its dominance should be indicative of invasion impairment.