There is growing concern regarding cadmium (Cd) exposure through rice consumption. Compared with alternate wetting and drying (AWD), continuous flooding (CF) is usually considered as an effective approach for reducing Cd enrichment in rice but increases the risk of pollution from arsenic (As). In this study, the field trial was conducted to investigate remediation effects of two water management (CF and AWD) techniques on Cd pollution in rice in typical japonica rice cultivation areas with varied soil pH levels. The results indicate that soil pH was a crucial factor in regulating CF-mediated Cd/As accumulation and migration in rice plants, and grains at all stages of rice growth. In acidic fields, compared with AWD, the use of CF reduced the accumulation of Cd in plants during the tillering stage; CF during the milk stage promotes the risk of contamination of Cd in rice grains and any form of As in plants and inhibits the content of any forms of As in grains. During the mature stage, CF reduced the levels of Cd in the plants and grains while promoting the accumulation of As(V) and total As(T-As) in plants and As(III) in grains. In alkaline fields, compared with AWD, CF during the tillering stage promoted the accumulation of various forms of As in plants. During the milk stage, CF increased and decreased the Cd content in plants and grains, respectively, and reduced the accumulation of T-As in plants and As(III) in grains; during the mature stage, CF promoted the accumulation of Cd in plants and grains, induced the accumulation of T-As plants, and inhibited the accumulation of any form of As in grains. From the perspective of food safety, the impact of CF conditions on the accumulation of Cd and As in rice from acidic fields exhibited a pattern of reduction in Cd and increase in As during the maturity period, as compared to that on the AWD. Conversely, CF increased the Cd risk while simultaneously reducing the As accumulation in rice grains to a safe level in alkaline fields. CF is not recommended as a remediation strategy for Cd pollution in rice in low Cd pollution areas, but it can be considered as a potential strategy for As pollution remediation in rice in alkaline fields with low Cd pollution.