High arsenic (As) concentration in groundwater potentially poses a serious threat to the health of local residents in southwestern Taiwan. Although the As release to groundwater is responsible for the reducing bacteria-mediated reductive dissolution of As-rich Fe hydroxides, the influences of FeRB and different organic substrates on As and Fe mobility and transformation were rarely discussed. An experiment that involved As-adsorbed synthetic amorphous Fe(III) hydroxide (HFO) and the inoculation of in situ Fe-reducing bacteria (FeRB) was performed to evaluate the contribution of FeRB to the As mobility and transformation. The batched experiment of As-free HFO showed that the reducing bacteria rapidly induced the reduction of amorphous Fe oxyhydroxide to Fe(II) by reductive dissolution of HFO and formation of Fe-citrate complexation. For aqueous As(V) reduction experiment, arsenate was effectively reduced to As(III) by the facultative anaerobic bacterium in the cultured FeRB. In the experiment of As-containing HFO reduction, the aqueous As(V) acts as an electron acceptor and reduced to As(III) after the reductive dissolution of Fe(III) on HFO. However, the increase in the As(III) concentrations with time for various organic substrates in the As-adsorbed HFO-reducing experiment differ from the rates of As(V) reduction with various organic substrates in the As(V)-reducing experiment. The decrease in sorption sites by coupled reductive dissolution of HFO and the competitive desorption of small molecular organic carbon is apparently the important factor of As mobility. For large molecular organic carbon (i.e., citrate), the significant contribution of citrate on As mobility is the complexation of iron citrate. A working hypothesis model of As biogeochemical cycling is proposed to illustrate the relevant processes in the groundwater aquitard of southwestern Taiwan.