In order to assess the influence of long-term irrigation of polluted river water on the ecological health of the rice fields in the low reach of Liaohe River Plain, a series of environmental samples and biological samples in rice fields, including sediments, paddy soils, mitten-handed crabs (Eriocheir sinensis), loaches (Misgurnus anguillicaudatu) and frog (Hoplobatrachus tigerinus), were collected from the area far away from industrial zones, and polychlorinated biphenyls (PCBs) and organochlorine pesticides (HCH, DDT, HCB and Mirex) were analyzed by high resolution gas chromatography coupled with high resolution mass spectrometry (HRGC/HRMS). The comparison of pollutant concentrations and profiles verified that the significant contribution of river water irrigation to PCBs contaminations in paddy soils and the mutual influence of organochlorine pesticide contamination between river sediments and paddy soils. Bioaccumulations of PCBs and organochlorine pesticides in mitten-handed crabs and loaches were site-specific, suggested that they were both the good indicators of ecosystem health. Mitten-handed crabs had the highest capacity to accumulate PCBs and organochlorine pesticides, and also they had the strong ability to degrade these pollutants in their bodies, especially for DDT and HCH. The biota-soil accumulation factors (BSAF) of HCH, DDT, Mirex, HCB Σ Σ and PCB Σ s in mitten-handed crab were calculated to be 24.5, 15.3, 122.2, 28.1 and 54.6, respectively. In view of the strong bioaccumulation ability, the health risk should be concerned for the cultivation of mitten-handed crabs in paddy fields in the low reach of Liaohe River Plain.