Chromium (Cr) is an expression toxic metal and is seriously released into the soil environment due to its extensive use and mining. Basalt is an important Cr reservoir in the terrestrial environment. Cr in paddy soil can be enriched by chemical weathering. Therefore, basalt-derived paddy soils contain extremely high concentrations of Cr and can enter the human body through the food chain. However, the water management conditions’ effect on the transformation of Cr in basalt-derived paddy soil with high geological background values was less recognized. In this study, a pot experiment was conducted to investigate the effects of different water management treatments on the migration and transformation of Cr in a soil–rice system at different rice growth stages. Two water management treatments of continuous flooding (CF) and alternative wet and dry (AWD) and four different rice growth stages were set up. The results showed that AWD treatment significantly reduced the biomass of rice and promoted the absorption of Cr in rice plants. During the four growth periods, the root, stem and leaf of rice increased from 11.24–16.11 mg kg−1, 0.66–1.56 mg kg−1and 0.48–2.29 mg kg−1to 12.43–22.60 mg kg−1, 0.98–3.31 mg kg−1and 0.58–2.86 mg kg−1, respectively. The Cr concentration in roots, stems and leaves of AWD treatment was 40%, 89% and 25% higher than CF treatment in the filling stage, respectively. The AWD treatment also facilitated the potential bioactive fractions conversion to the bioavailable fraction, compared with the CF treatment. In addition, the enrichment of iron-reducing bacteria and sulfate-reducing bacteria with AWD treatment also provided electron iron for the mobilization of Cr, thus affecting the migration and transformation of Cr in the soil. We speculated that the reason for this phenomenon may be the bioavailability of Cr was affected by the biogeochemical cycle of iron under the influence of alternating redox. This indicates that AWD treatment may bring certain environmental risks in contaminated paddy soil with high geological background, and it is necessary to be aware of this risk when using water-saving irrigation to plant rice.