Archaeological investigations at prehistoric site CA-MRN-254 at the Dominican University of California in Marin County, California, revealed evidence of Native American occupation spanning the past 1,800 years. A dominant source of food for the inhabitants in the San Francisco Bay area was the intertidal, quiet-water dwelling blue mussel (Mytilus trossulus), although rare occurrences of the open coast-dwelling California mussel (Mytilus californianus) suggest that this species was also utilized sporadically. On rare occasions, cultural horizons at this site contain abundant sediment-filled casts of the smaller mussel Modiolus sp. These casts were formed soon after death when the shells filled with sediment and were roasted along with living bivalve shellfish for consumption. Thin sections of these mussel casts display sedimentological and microbiological constituents that shed light on the paleoenvironmental conditions when they were alive. Fine-grained sediment and pelletal muds comprising these casts suggest that the mussels were collected in a low energy, inner bay environment. The rare presence of the diatoms Triceratium dubium and Thalassionema nitzschioides indicate more normal marine (35 psu) and possibly warmer conditions than presently exist in San Francisco Bay. Radiocarbon dating of charcoal associated with the mussel casts containing these diatoms correlates with a 600-year period of warming from ca. A.D. 700–1300, known as the Medieval Climatic Anomaly. Results of this mussel cast study demonstrate that they have great potential for providing paleoenvironmental information at this and other archaeological sites.