Intake of groundwater with arsenic (As) concentrations exceeding the World Health Organization standard of 10 mu g L(-1)adversely impacts over 100 million people worldwide. Geogenic As contaminated groundwater within central Yangtze River Basin has recently been reported, but the variations within different depths of aquifers are not commonly observed and the processes controlling As variations have yet to be resolved. Here we report the significant As variations within two different depths (10 m and 25 m) of shallow multi-level alluvial aquifers at Jianghan Plain, a floodplain in the central Yangtze River Basin, which is also a recently discovered geogenic As affected area with cases of waterborne arsenicosis. The multi-year monitoring of aquifer chemistry results show that the As concentrations increase with the Fe(II) concentrations when As contents are relatively lower (<200 mu g L-1 ) in upper phreatic aquitard (at 10 m depth), while decrease with Fe(II) concentrations when As contents are much greater in lower confined aquifer (at 25 m depth), and the highest is up to 1070 mu g L-1 . Iron isotope analysis were conducive to characterize Fe cycling in the aquifers and thus illustrate geochemical processes controlling As mobilization of shallow groundwaters. Results showed that groundwater is generally enriched in isotopically light Fe with delta Fe-56 values between - 1.60 parts per thousand and + 0.06 parts per thousand (median - 0.55 parts per thousand). In the upper phreatic aquitard, microbial reductive dissolution of As-associated Fe(III) oxides, hydroxides and oxyhydroxides is the major process controlling As concentrations lower than 200 mu g L-1 . The reduction process could lead to the increasing As concentrations with the gradually increasing delta Fe-56 values, and a positive correlation between Fe and delta Fe-56, and between dissolved As and delta Fe-56 values is observed, respectively. In strongly reducing conditions as the lower confined aquifer, jointly microbial reduction of sulfate promotes the As mobilization through HS abiotic reduction of Fe(III) minerals, resulting in As concentrations greater than 200 mu g L-1 . These findings could provide new insights for differentiating the major factors controlling As mobilization at different depths of aquifers, and provide better water managements for similar geogenic As-affected shallow alluvial aquifers.