Scaphopods are found exclusively in soft silty marine sediments, into which they burrow in search of food. Some species burrow only a short distance into the mud, leaving their narrow apical end protruding from the sediment surface; this position has become a classic illustration in many treatments of the group. Many species, such as Gadila aber-rans, however, burrow to depths several times their body length.

While most species favor foraminiferans as food, and thereby have a preference for habitats with high densities of these shelled protists, some species successfully inhabit other areas by broadening the variety of microorganisms they eat. While scaphopods are considered relatively uncommon members of the benthic communities in which they live, in some areas they can reach relatively high densities. For example, Rhabdus rectius reaches almost 60 individuals per square yard (0.76 square meter) around Sandford Island off the western coast of Vancouver Island, British Columbia.

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