To investigate the effects of water management and silicon application on cadmium (Cd) uptake by rice plants and the bioavailability of Cd in paddy soil, a pot experiment was conducted. The experiment included different water management practices and silicon fertilizer treatments: conventional water management (CK), alternating wet and dry conditions (IF), and long-term flooding (CF), each combined with silicon fertilizer (CK+Si, IF+Si, and CF+Si). The results showed that, compared to CK, Cd content in roots, stems, leaves, and brown rice under CF+Si treatment decreased by 61.6% (P < 0.05), 82.6% (P < 0.05), and 60.5% (P < 0.05), respectively. Under the same water management conditions, silicon fertilizer application reduced Cd content in roots, stems, and brown rice by an average of 43.1%, 38.7%, and 15.1%, respectively. Compared to conventional water management, alternating wet and dry conditions increased soil available silicon and available Cd, while long-term flooding reduced both. The application of silicon fertilizer increased soil available Si content while reducing soil available Cd, soil pore water Cd, and exchangeable Cd (Exc-Cd). Under the same water management conditions, silicon fertilizer application decreased Exc-Cd and carbonate-bound Cd (Carb-Cd) while increasing residual Cd (Res-Cd). In terms of water management, Cd content in roots, stems, leaves, and brown rice showed a significant positive correlation with soil pore water Cd and Exc-Cd. Moreover, Cd content in all plant parts was significantly positively correlated with soil available Cd, pore water Cd, and Exc-Cd across all treatments. The combination of silicon fertilizer and water management significantly altered soil available Cd, pore water Cd, and Exc-Cd content, thereby affecting Cd uptake by rice plants. In conclusion, long-term flooding combined with silicon fertilizer is a recommended agronomic management strategy for cadmium-contaminated farmland.