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Blue mussels (Mytilus edulis) are ecosystem engineers with strong effects on species diversity and abundances. Mussel beds appear to be declining in the Gulf of Maine, apparently due to climate change and predation by the invasive green crab, Carcinus maenas. As mussels die, they create a legacy of large expanses of shell biogenic structure. In Maine, USA, we used bottom traps to examine effects of four bottom cover types (i.e., live mussels, whole shells, fragmented shells, bare sediment) and wind condition (i.e., days with high, intermediate, and low values) on flow-related ecosystem processes. Significant differences in transport of sediment, meiofauna, and macrofauna were found among cover types and days, with no significant interaction between the two factors. Wind condition had positive effects on transport. Shell hash, especially fragmented shells, had negative effects, possibly because it acted as bed armor to reduce wind-generated erosion and resuspension. Copepods had the greatest mobility and shortest turnover times (0.15 d), followed by nematodes (1.96 d) and the macrofauna dominant, Tubificoides benedeni (2.35 d). Shell legacy effects may play an important role in soft-bottom system responses to wind-generated ecosystem processes, particularly in collapsed mussel beds, with implications for recolonization, connectivity, and the creation and maintenance of spatial pattern.