Irrigating rice paddy fields with groundwater containing iron is standard practice for dry croplands replanted to rice in northeast China. To assess the impact of paddy field drainage on the receiving natural wetlands, vertical migration and distribution of dissolved iron in the soil–plant system with acidic dissolved iron addition were investigated in the Carex lasiocarpa marsh soil columns (diameter 35cm, height 65cm) of the Sanjiang Plain. The experiment was designed as four sequential stages: (1) iron-free leaching, (2) neutral iron addition using FeSO4 (100mgL−1 of iron concentration), (3) acidic iron addition using FeSO4 and HCl (200mgL−1 of iron concentration, pH adjusted to 3.56) and (4) iron-free leaching. After the experiment, the iron distribution within a natural wetland ecosystem was quantitatively observed. The results showed that pH and Eh in the soil columns were affected more by water table fluctuations than acidic addition. Effects of iron addition on the dissolved iron in soil solutions decreased with increasing soil depth, and the vertical migration rates in 20–30cm layer (AG horizon) and 30–50cm layer (G horizon) were 0.58 and 0.56mmmin−1, respectively. Doubling the iron addition did not increase the iron in soil solutions significantly. Only a small part of added iron (5.7%) drained out, while the majority was retained in soil (69.4%) and plant biomass (24.8%). Soil manganese and nitrogen were positively affected by acidic iron addition, while the effects on carbon and phosphorus were not significant.