Extensive application of neonicotinoid insecticides (NNIs) in agricultural production has resulted in widespread contamination of multiple environmental media. To investigate the occurrence and fate of NNIs in the largest marsh distribution area in Northeast China, an integrated ecosystem covering farmlands, rivers, and marshes, referred to as the farmland-river-marsh continuum in this study, was chosen for soil, water, and sediment sampling. Five NNIs were detected, with imidacloprid (IMI), thiamethoxam (THM), and clothianidin (CLO) being the most frequently detected ones in different samples. Concentrations of target NNIs in soil, surface water, and sediment samples were 2.23-136 ng/g dry weight (dw), 3.20-51.7 ng/L, and 1.53-8.40 ng/g dw, respectively. In soils, NNIs were detected more often and at higher concentrations in upland fields, while the concentration of NNIs in the soybean-growing soils (71.5 ng/g dw) was significantly higher than in the rice-growing soils (18.5 ng/g dw) (p < 0.05). Total concentration of NNIs in surface water was lower in the Qixing River channel than inside the marsh, while that in sediments showed an opposite trend. Total migration mass of IMI from approximately 157,000 ha of farmland soil by surface runoff was estimated to be 2636-3402 kg from the application time to the sampling period. The storage of NNIs in sediments was estimated to range from 45.9 to 252 ng/cm2. The estimated environmental risks, calculated as the risk quotients (RQs), revealed low risks to aquatic organisms (RQs <0.1) from the residual concentrations of NNIs in water.