During coal mining activities, a lot of coal gangue is produced, which usually contains high mercury (Hg) concentrations as well as the acid mine drainage (AMD) generator of pyrite. In the present study, the total mercury (THg) and methylmercury (MeHg) in gangue, water, sediment, paddy soil, and rice samples, collected from abandoned coal mining areas, were analyzed. Results showed that the THg concentrations ranged from 0.37 to 35 mg/kg (11？±？8.4 mg/kg) and 0.15 to 19 mg/kg (2.0？±？3.9 mg/kg) in gangue and sediments, respectively. For paddy soils, the THg concentrations and MeHg varied from 0.16 to 0.91 mg/kg and 0.71 to 11 ng/g, respectively. Rice samples exhibited wide concentration ranges of THg (3.0–22 ng/g) and MeHg (0.71–8.9 ng/g). Sequential extraction of Hg revealed that the nitric acid-extractable state Hg (F4) was the dominant Hg species in gangue and sediment, while humic acids state Hg (F3) was the dominant form in paddy soil. Compared with gangue, higher percentages of F3 and the residual state Hg (F5) in both sediment and soil samples implied the transformation of F4 to F3 and F5 during transportation. Soil n-HAs (the difference between the total organic carbon and humic acids) were positively correlated with both THg and MeHg in soil and rice, indicating that n-HAs enhance Hg bioavailability under acidic conditions. Further studies should be conducted to reveal the factors influencing the transformation of different Hg fractions, providing ideas on decreasing the bioavailability of Hg in coal mining areas.