Salinity, temperature, and substrate are generally the primary factors controlling the distribution of marine benthonic invertebrate organisms. The bottom water in the western basin of the Champlain Sea was esentially cold throughout the marine episode and hence in most cases water temperature was not a significant controlling factor. However, warmer boreal water did migrate into the eastern part of the study area during the latter part of the marine episode and was characterized by the Mya arenaria association. The dominant species of the macrafaunal associations and microfaunal assembledges occur in large numbers in boath coarse and fine grained marine sediments. Hence, substrate was generally not a controlling factor. Exceptions to this are Portlandia arctica and Cytheropteron pseudomontrosiense which are found mainly in clay and Balanus hameri and Elphidium incertum/asklundi which occur almost exclusively in pebbly sandy clay and pebbly sand. Because water temperature and nature of substrate were not major controlling factors, the assembledge ocurrence must have been controlled primarily by salinity. The sucession of assembledges indicate that the salinity of the bottom waters of the Champlain Sea decreased with time.