Benthic ecosystems at temperate and high latitudes experience marked seasonal variation in the environmental factors affecting nutrient remineralization processes both directly and indirectly through their effects on the benthic communities. The invasive polychaete genus Marenzelleria spp. represents new functionality in Baltic Sea sediments through its deep burrowing and extensive gallery formation, thus possibly greatly affecting the benthic oxygen and nutrient fluxes. We assessed the seasonal contribution of Marenzelleria spp. to fluxes of solutes in monthly field measurements at two sites, 10 and 33 m deep, in the northern Baltic Proper over a year. In general the fluxes of inorganic nutrients and oxygen were higher during summer than during winter and the seasonal variation was more pronounced at the deeper, more biologically active site. By using variation partitioning we were able to demonstrate that Marenzelleria and other macrofauna could account for up to 92 % of the variation in the fluxes depending on the site and season. Fauna was the most important in predicting the fluxes in spring when the sediment organic content and the abundance of juvenile Marenzelleria spp. were highest, while during e.g. winter the influence of Marenzelleria spp., even though abundant, on solute fluxes was negligible. The results from this study have implications for management, and, importantly, for the modelling of nutrient budgets often based on values from studies conducted during the summer period only, thus possibly greatly miscalculating the annual nutrient fluxes.