Rivers transport large amounts of allochthonous organic matter (OM) to the ocean every year, but there are still fundamental gaps in how allochthonous OM is processed in the marine environment. Here, we estimated the relative contribution of allochthonous OM (allochthony) to the biomass of benthic and pelagic consumers in a shallow coastal ecosystem in the northern Baltic Sea. We used deuterium as a tracer of allochthony and assessed both temporal variation (monthly from May to August) and spatial variation (within and outside river plume). We found variability in allochthony in space and time and across species, with overall higher values for zoobenthos (26.2 +/- 20.9%) than for zooplankton (0.8 +/- 0.3%). Zooplankton allochthony was highest in May and very low during the other months, likely as a result of high inputs of allochthonous OM during the spring flood that fueled the pelagic food chain for a short period. In contrast, zoobenthos allochthony was only lower in June and remained high during the other months. Allochthony of zoobenthos was generally higher close to the river mouth than outside of the river plume, whereas it did not vary spatially for zooplankton. Last, zoobenthos allochthony was higher in deeper than in shallower areas, indicating that allochthonous OM might be more important when autochthonous resources are limited. Our results suggest that climate change predictions of increasing inputs of allochthonous OM to coastal ecosystems may affect basal energy sources supporting coastal food webs.