A field experiment investigating the structuring effect of filamentous green algae on macrofaunal abundance, including functional feeding groups, was performed in a shallow (1 m) soft bottom bay on the Swedish West Coast. Temporal macrofaunal changes were investigated at three occasions under simulated moderate algal disturbance, using algal filled net-bags attached over the sediment. The moderate algal disturbance was also compared to a simulated high algal disturbance where cages were filled with algae. Abundance of suspension feeders and surface detrivores decreased significantly in the sediment after 3 weeks of exposure to high algal disturbance in cages compared to control sediment, but did not change in abundance from moderate disturbance under algal net-bags after this time. However, total macrofauna, suspension feeders and surface detrivores had significant lower abundance in the sediment under algal net-bags compared to controls, when all three occasions were included. Total abundance per unit area in the algae and its underlying sediment was significantly higher in the net-bag treatment compared to total macrofauna in algal cages and controls. This was mainly due to high abundance among algae. Burrowing detrivores and predators had higher abundance among algae in the net-bags compared to algae in the cages. High abundance of macrofauna recorded among algae in the net-bag treatment could be due to filtering of larvae, post settlement redistribution or vertical migrations. In a laboratory experiment, juvenile Cerastoderma spp. and Corophium volutator migrated vertically into filamentous algae from sediment covered by an algal mat. C. volutator and adult Cerastoderma edule also had the ability to perform small-scale horizontal migrations from algae covered sediment. Suspension feeding bivalves are major contributors to production of the infauna in shallow soft bottoms, are important food for epibenthic predators and may functionally stabilise shallow marine soft bottoms. Decreases in recruitment and abundance of such an important functional group may thereby alter function and trophic relationships on shallow soft bottoms.