Organic matter (OM) resources shape not only the trophic diversity of benthic communities but also the diversity of benthic functional traits. The resulting community structure has a direct effect on many ecosystem processes and functions. Still, the relationship between functional diversity of marine benthos and its trophic diversity in response to the variability of food remains poorly investigated. To explore this relationship we focused on the assessment of various facets of macrobenthic diversity in two temperate coastal areas (southern Baltic Sea) characterized by similar species pool and habitat properties but different OM sources and supplies. We also identified spatio-temporal patterns of functional structure and assessed, which OM properties had the strongest influence on benthic communities. In our study, functional space dispersion followed isotopic space dispersion, reflecting the positive relationship between food variability and ecological functions of benthic communities. Moreover, functional structure in shallow areas was more location-specific in comparison to deeper areas, and this was significantly related to OM parameters. Higher OM variability close to the river mouth prevented the community from becoming dominated by one specialized species, whereas limited OM supply at shallow open coast lowered the diversity by enabling stronger competitor to dominate the community. In more offshore areas, local OM variability ceased and hence, communities tended to reflect similar trophic and functional patterns. Our study demonstrates that functional and isotopic diversity approaches can be effectively combined to better understand mechanisms driving benthic community structure and confirm that greater variability in OM supply increases diversity of benthic communities.