The conditions which existed in the Champlain Sea were continuously fluctuating, as a result of the close proximity of the Laurentide ice sheet. Temperature and salinity never really experienced consistent states, due to the huge volume of melt water, and the response to the land to the unloading of the glacial ice. It is believed that in the early stages of the sea both temperature and, salinity were low. This assumption is supported in the fossil assemblages. A number of assemblages have been found that contain Hiatella, which is tolerant to low salinities, and require summer temperatures lower then 11 degrees Celsius to reproduce. It is difficult to pinpoint a specific average salinity for the entire sea, however 8 parts per thousand seems to be a good estimation for such large variances. Also, temperature can not be given a specific value, although the fossil record demonstrates a cool early phase with a warming trend throughout it's existence.
A high energy environment existed in the region, and the system was always in a state of flux. The Champlain Sea never had a chance to settle, since it's disappearance began right from the moment it was created.