Mussels are well-known ecosystem engineers in soft-bottom systems. Mytilus edulis beds have myriad effects on sediment, benthic organisms, and ecosystem processes such as hydrodynamic transport of sediment and animals. When mussels die, they may leave behind massive amounts of whole (empty) and fragmented shells. The legacy effects of this long-lasting biogenic material (i.e., shell hash) on benthic systems are poorly understood. We measured percent cover values of 4 bottom cover types, i.e., live mussels, whole shells, fragmented shells, and bare sediment, at the mussel bed in Carrying Place Cove, Harrington, Maine, USA, and examined their effects on sediment characteristics, community structure of macrofauna and meiofauna, and ecosystem processes of sediment flux and dispersal of postlarval macrofauna and meiofauna. We predicted that live mussels are the cover type with the greatest effects compared to bare sediment, followed by fragmented shells and then whole shells. We discovered mostly bare sediment, substantial cover of whole and fragmented shells, and almost no live mussels in what had in past years been a robust bed. We found significant univariate and multivariate differences in sediment and animals across cover types, especially for meiofauna. Fragmented shell material in particular may be an important driver in this system. Our results are the first to quantify the 4 mussel bed cover types and demonstrate their effects. Mussel beds in the Gulf of Maine have experienced severe declines in the past two decades, attributed primarily to climate change and the invasive green crab, Carcinus maenas. Our results may be useful in predicting the responses of soft-bottom systems as intact mussel beds die off, leaving large areas of bare sediment and shell hash.