Surficial materials were mapped on the bottom of Cobscook Bay, ME, through aerial photography of intertidal habitats, side-scan sonar, and seismic reflection profiling of subtidal regions. Like many other estuaries in northern New England, this rocky, macrotidal estuary has only slight riverine input and contains an abundance of till and fine-grained glacial-marine sediment. Contrary to conceptual models of estuarine sediment and habitat distribution, grain size does not become finer and habitats lower in energy in a landward direction within the estuary. The irregular shoreline shape, imparted by bedrock, forms a series of narrow constrictions separating broad bays. More than 70% of the bottom of the estuary is floored by gravel and rock; mud deposits are located in shallow-water coves throughout the Bay and in two large deposits in the Central Bay. Here, circulation models predict two large gyres form because water cannot pass through a bedrock constriction quickly enough. Natural gas is present in sufficient quantities in the sediment column to facilitate sediment mass movements near the mud deposits. Almost 60% of the intertidal zone is composed of mudflats that are uniformly distributed within and along the outside margin of the Bay, with increasing abundance of bedrock in a landward direction. Small beaches occur wherever coarse-grained glacial sediment erodes from bluffs. These observations depart from existing conceptual models of estuarine sediment distribution based on coastal plain estuaries and suggest that better understanding of biotic habitat or contaminant distribution in rocky glaciated estuaries will require more localized models. These estuaries appear more complex than coastal plain estuaries because of the unique outcrop pattern of bedrock and glacial deposits in each bay.