We explored nutrient distribution in water and heavy metal contamination in sediments after rice harvest in a rice-shrimp co-cropping system. Additionally, we assessed aquatic ecological risks by evaluating molecular ammonia toxicity and heavy metal levels in rice-shrimp fields and systematically analyzed the ecotoxicity of nutrients and heavy metals in water in the co-cropping system by monitoring physicochemical indices in water during the late cultivation period in four rice and shrimp co-cultivation fields. After rice harvesting, the water showed high pH (9.25) and the total nitrogen concentration, ammonia nitrogen, and COD reached 14.15, 11.49, and 92.01 mg/L, respectively. In perennial rice-shrimp co-cropping systems, elevated levels of ω_As (16.21 mg·kg^–1) and ω_Cd (0.20 mg·kg^–1) were found in sediments, exceeding natural baseline levels by 2.35 and 1.72 fold, respectively. Levels of other heavy metals were lower, in addition, the concentration of heavy metal was lower than the baseline levels of the sediments. The potential ecological risk index and our potential biological toxicity evaluation revealed low ecological risks posed by heavy metals in rice-shrimp co-cropping system sediments, which can be attributed to mineral elements required for Procambarus clarkii culture. In conclusion, co-cultivating rice with shrimp can potentially mitigate soil heavy metal pollution.