Studies covering combined effects of agronomic management strategies and their interactions for safer rice production in multiple heavy metal [cadmium (Cd) and lead (Pb)] and metalloid [(arsenic (As)] contaminated soil are rare. Therefore, the effectiveness of phosphorus (P) or silicon (Si) addition together with soil water management (flooded or aerobic) in a soil contaminated with multiple heavy metals was tested in a pot experiment for 8 weeks. Growth of rice was retarded under flooding (27%) compared to aerobic conditions, and application of P led to recover the reduction in growth. Aerobic and flooded water managements could decrease 66% As and 84% Cd concentrations in rice tissues, respectively. Applications of P or Si could decrease only 22% As (only under flooded condition) and 24% Cd (only under aerobic condition) in rice tissues. Accumulation of Pb in rice was not observed. Aerobic soil lowered the concentrations of As, Cd and Pb in the soil solution when compared to flooding. Moreover, As and Pb concentrations in soil solution increased with time while that of Cd declined. Appropriate water management was the most efficient in reducing heavy metals and metalloids accumulation in rice seedlings while the effects of P or Si were marginal.