Land application of organic manure, crop residue, and biosolid, an important means for the disposal and recycling of wastes, has been shown to significantly increase the amount of dissolved organic matter (DOM) in soil. However, limited information is available on the dynamics of DOM, the concentration is usually expressed by dissolved organic carbon (DOC), and its influence on Cd behaviors in paddy soil amended with and without organic materials during rice (kinmaze) growing season. In this study, in situ field experiments were conducted to investigate the dynamics of DOC in paddy soil amended with green manure (GM), pig manure (PM), and chemical fertilizer (F) and its effect on Cd mobility and bioavailability. The results showed that DOC concentrations in soil solutions extracted from different depths were higher in GM and PM plots than those in F plot, and DOC concentrations all declined with time and rice growth. DOC concentrations in the root zone soil for all treatments were higher than those in the non-root zone due to root exudation and the higher pH value. The temporal dynamics of DOC in the root zone were found to be correlated to rice growth stage, as DOC concentrations decreased in the initial stage (week 1 to 6) of rice seedling and then gradually increased and reached the highest levels with 30.42 mg DOC L−1 for GM, 28.88 mg DOC L−1 for PM, and 19.19 mg DOC L−1 for F at rice heading and flowering stage (week 10), hereafter decreased again until when the rice was harvested. However, soil DOC in the non-root zone exhibited a continuous decrease trend and remained at a relatively low level after week 10 with 15.36 mg DOC L−1 for GM, 15.31 mg DOC L−1 for PM, and 8.43 mg DOC L−1 for F. The dynamics of water soluble Cd displayed statistically significant positive relationship with DOC (r 0.01 = 0.765, n = 9) regardless of soil depth and root presence/absence, suggesting that DOC enhanced the mobility and transport of through the formation of Cd-DOC complexes. As a result, DOC could increase the potential uptake of Cd by rice as well as the downward Cd migration to deeper soil. In these experiments, the uptake of Cd by rice grown in the GM and PM plots reached 5.55 and 3.71 mg plot−1, respectively, which were much higher than that in the F plot with 1.88 mg plot−1. The amounts of Cd downward migration were 17.0 mg plot−1 for GM plot, 14.74 mg plot−1 for PM plot, and 4.13 mg plot−1 for F plot, respectively. It could be concluded that the application of green manure and pig manure to Cd-contaminated paddy soil will increase the risk of Cd uptake by rice and Cd downward migration into groundwater. For this reason, care should be taken when organic manures was applied to contaminated soil to remediate or alleviate soil pollution and maintain soil fertility as well as provide nutrients for plant growth.