In this study we describe community parameters such as densities, biomasses, species composition, feeding modes and normalized biomass size-spectra (NBSS) of macrobenthic invertebrate communities from three stations located in the Baker Fjord obtained on four seasonal campaigns in 2008 and 2009. The macrobenthic communities were dominated by small-bodied polychaetes (Paraonidae, Capitellidae and Cirratulidae) characterized by continuous year-round breeding, short life-spans, and fast turnover rates, which in turn regulated the standing stock in the communities. Principal component analysis and multiple-regression analysis demonstrate the distribution of macrobenthic communities in the study area to be mainly controlled by few local environmental conditions. Macrofaunal densities, diversity and feeding modes were significantly correlated with the total organic carbon (TOC; R2 = 0.74; P < 0.001) and chlorophyll-a (Chl-a; R2 = 0.55; P < 0.05) content in the sediments. This study also suggests that feeding modes and NBSS can be used to detect and follow possible changes caused by natural perturbations such as glacial lake outburst floods or anthropogenic stressors associated with ecological impacts generated by the construction and operation of hydroelectric power stations in the Baker River.