Salinity is a key environmental factor for aquatic organisms for survival, development, distribution, and physiological performance. Salinity fluctuation occurs often in estuary and coastal zones due to weather, tide, and freshwater inflow and thus heavily affects coastal marine aquaculture. The northern quahog Mercenaria mercenaria is an important aquaculture species along the Atlantic coast in the US, but information on the effects of salinity stress on physiological, immunological, and molecular responses is still scarce. The goal of this study was to investigate cellular and molecular responses through challenges of long-term hypo- and hyper-salinities in northern quahogs. The objectives were to: 1) measure the survival of market-sized quahogs under a three-month salinity challenge at 15 (hyposalinity), 25 (control), and 35 ppt (hypersalinity); 2) determine cellular changes of hemocytes through analysis of immune functions; 3) determine changes of the total free amino acid concentration in gills, and 4) evaluate the molecular responses in gills using RNAseq technology with qPCR verification. After a three-month salinity challenge, no mortality was observed, and increases in body weight were identified with a significantly higher increase in the hypersalinity group. Northern quahogs equilibrated their hemolymph osmolality with the ambient seawater and were verified to be osmoconformers. Significant differences were observed in total hemocyte concentration, lysosomal presence, ROS production, and phagocytic rate, but no differences were found in cell viability. The total free amino acid concentration within gills was positively correlated to water salinity, indicating amino acids were critical organic osmolytes. The transcriptome of gills using RNAseq revealed differential expression genes (DEG) encoding amino acid transporters (SLC6A3, SLC6A6, SLC6A13, SLC25A38), ion channel proteins (T38B1, GluCl, ATP2C1), and water channel protein (AQP8) in hyposalinity or/and hypersalinity groups, indicating these genes play critical roles in intracellular isosmotic regulation. Overall, the findings in this study provided new insights into osmoregulation in northern quahogs.