Qixing River wetland is very representative of the marsh environment of Sanjiang Plain, northeast China. The wetland plays an important role in maintaining ecological service functions especially for protecting migratory birds. Despite Qixing River wetland being impacted by a number of diffuse and point sources of pollution (primarily from agricultural activities), a comprehensive survey of heavy metal exposure risk to migratory birds has never been undertaken. Identifying heavy metals exposure risk is significant for further improving the protection scheme of migratory birds. In the present study, the comprehensive water pollution index (WPI) and geo-accumulation index (I-geo) were calculated to assess the degree of contamination of water and sediments, respectively. Single-pollutant exposure metrics (HQ) were applied to measured concentrations in order to estimate the heavy metal exposure risk to migratory birds. In addition, an integrated hazard index (HI) was derived to assess the comprehensive risk of exposure to multiple heavy metals and associated risk threshold values calculated. The decreasing trends of average concentration of heavy metals were Zn > Cr > Ni > Cu > Pb > Cd in sediments and Zn > Cr > Pb > Ni > Cu > Cd in water. Concentrations of Cr were significantly elevated compared to the threshold of Aquatic Life Water Permissible Limits (AWPL) and Sediment Quality Guidelines (SGQ) (p < 0.01), thus may pose negative impacts to the aquatic ecological system. Values of WPI indicated 'Clean' status for more than 85% sampling sites with Zn accounting for 58% of the value of the WPI. Most of the sediment sampling locations were deemed to be 'Clean' or 'Low' status as defined by I-geo with Zn and Cd (mainly derived from agricultural sources) identified as the dominant indicators of pollution. Comprehensive exposure risk assessment indicated 'Moderate' risk (HI > 1) status for local populations of Eurasian Spoonbill. Despite the majority of heavy metals (except for Zn) being assigned 'Clean' or 'Low' pollution status, the elevated hazard quotient (HQ > 3) associated with Cr enhanced overall values of HI, especially for nestlings, indicating that current pollution control measures are insufficient for the protection of migratory birds. This study has supplemented current knowledge of the impacts of agriculture on wetland ecosystems and provides evidence that exposures of migratory birds to some heavy metals may exceed 'safe' levels. This study thus provides a scientific rationale for determining the safe feeding water depth for migratory birds.