The EC Water Frame Directive (WFD) states that all coastal water bodies must achieve ‘good ecological status’ by the year 2015. A range of different classification methods have been developed and used to define ecological status to support the WFD. The aim of this study was to compare the effects of using two different mesh sizes of sieve (1.0 and 0.5 mm) on zoobenthic assemblages and on the ecological status of benthic macrofauna (using the Brackish water benthic index, BBI) in three ecologically distinct archipelago areas (Inner, Middle and Outer) in the Åland Islands, Northern Baltic Sea. We performed a biological trait analysis (BTA) to evaluate differences in the functional (trait) diversity of macrofauna collected using different mesh sizes and estimate the ecological relevance of mesh size. The results showed that sieve mesh size had significant effects on the recorded number of species, abundance, and total biomass of the zoobenthos. Small-bodied species and juveniles (e.g. Macoma balthica) were not observed when using a 1.0-mm mesh. The ecological status (sensu WFD) was only slightly affected by the mesh size, and all areas had good or high ecological status. BTA showed a difference in trait composition when using 0.5- or 1.0-mm mesh, particularly in the Outer area, where the proportion of small-sized species was high. Our results highlight how biological traits, in addition to species number and biomass, can play a key role when analyzing ecosystem structure for assessment and classification of coastal ecosystems. We show that combining traditional monitoring for the EU WFD with a functional analysis strengthens our ability to interpret environmental quality, and thus increases the precision of our advice for management purposes.