It has been suggested that herbivorous waterfowl may be important in shaping aquatic plant communities in shallow wetlands. As such, a shift from canopy forming pondweeds to bottom-dwelling charophytes in a formerly turbid pondweed dominated lake has been partly attributed to waterfowl herbivory. Here we study the separate and combined effects of both belowground herbivory in spring by whooper swans and Bewick ‘s swans, and grazing in summer by waterfowl and fish on the community composition in a shallow Baltic estuary during one year. The macrophyte community was dominated by charophytes (mainly Chara aspera) with Potamogeton pectinatus and Najas marina present as subdominants. Other species were rare. Both spring and summer herbivory had no effect on total plant biomass. However, P. pectinatus was more abundant in plots that were closed to spring and summer herbivores. N. marina was more abundant in grazed plots, whereas Chara spp. biomass remained unaffected. Probably belowground propagules of both C. aspera and P. pectinatus were consumed by swans but since C. aspera bulbils were numerous it may have compensated for the losses. P. pectinatus may not have fully recovered from foraging on tubers and aboveground biomass. Our results are in line with other studies in Chara dominated lakes, which found no effect of grazing on summer aboveground Chara biomass, whereas several studies report strong effects of herbivory in lakes dominated by P. pectinatus.