Purpose <p>Understanding how root activity responds to potentially toxic elements (PTEs) in reduced paddy soil is crucial for effectively applying in situ immobilization and minimizing their transfer to rice.</p> Methods <p>Using a rhizobox system, this study aims to investigate how rice rhizosphere redox processes influence soil chemistry, the bioavailability of arsenic (As) and cadmium (Cd), and their accumulation in polished rice under four soil amendments: phosphogypsum, bone meal, biochar, and guano.</p> Results <p>Rice cultivation with these amendment applications resulted in a slight decrease in rhizosphere pH and an increase in dissolved organic carbon (DOC) and electrical conductivity compared to bulk soil. These changes altered metal dynamics, resulting in higher bioavailable concentrations of As and Cd in the rhizosphere. Under rhizosphere conditions, all soil amendments, except bone meal, prevented further increases in the labile fractions of As and Cd relative to the control, rather than producing statistically lower values. Biochar resulted in the lowest As accumulation, while bone meal showed the lowest Cd accumulation in polished rice, although it slightly increased Mehlich-3 extractable As and Cd in soil. Pearson’s correlation analysis also revealed significant relationships between soil chemical parameters, particularly DOC, and bioavailable As and Cd.</p> Conclusion <p>Overall, these findings underscore the crucial role of rhizosphere chemistry under reduced paddy soil conditions in regulating the mobility and plant uptake of As and Cd. Managing rhizosphere redox conditions through the application of appropriate soil amendments offers a promising strategy for mitigating PTE contamination risks in flooded rice production systems.</p> Graphical abstract <p></p>