The aim of this study was to compare environmental pollution and ecological states of two different areas of the Songhua River areas: near Harbin City and Tongjiang City, located at a distance of about 500 km downstream. The anthropogenic pollution concentrations of heavy metals (HM) were determined. The results showed that concentrations of eight metals (Cd, Cr, Cu, Fe, Mn, Ni, Pb, and Zn) in the water were in the range of 0.001–0.588 mg/L for Tongjiang and 0.001–0.508 mg/L for Harbin, while that in sediments were in the range of 0.67–1575.37 mg/kg for Tongjiang and 0.07–5617.13 mg/kg for Harbin, respectively. Bivalves from tested sites exposed to environmental pollution exhibited significantly different physiological states. The latter was assessed using the method of physiological loading, based on measuring the recovery time (T_rec) of heart rate (HR) after removal of the load. T_rec in mussels from Harbin was recorded in the range of 151 to 234 min, while that from Tongjiang was only 115 min. Cd, Cu, Pb, and Zn in mollusk soft tissues were also determined for Harbin and Tongjiang, respectively. The metal pollution index (MPI) and bioconcentration factor (BCF) in the mollusks were calculated for each metal. BCF in the mussels from the Tongjiang area was lower than that from the Harbin area. Physiological testing, as well as the concentration of HM in water, and sediment, and also the bioaccumulation of HM in tissue showed that the ecological state of the Tongjiang area was better than that of Harbin. Apparently, after more extensive studies, a methodological approach of assessing the ecological state of water areas, based on physiological state testing of aboriginal mollusks, could be used in the monitoring of pollution effects in water bodies and streams.