The concentration of Cu (Copper) and Zn (Zinc) decreases upon flooded conditions of rice soil. To assess the effects of flooding and application of Cu and Zn coated urea on changes in Eh, pH and solubility of Cu and Zn, a glasshouse experiment was conducted at Universiti Putra Malaysia. Rice plants (30 days old seedlings of type MR-219) on two soils (riverine and alluvium and marine alluvium) were transplanted. Nine treatments with variable rates and combinations of Cu and Zn coated urea were applied. The sources of fertilizers were copper sulfate and zinc sulfate. Eh values decreased with flooding time in both soils. The changes of Eh values were more negative in control treatments and stabilized after 3 weeks of submergence. The Eh variation was not observed affectively in the treated soils however, soil pH increased with flooding time. During the 3rd week of submergence, pH was neutral (pH 7.0). In both soils, Cu and Zn treated soil showed lower Eh and higher pH values as compared to untreated soil. Concentration of Cu and Zn in soil solution decreased with flooding. The higher Cu and Zn contents in soil were recorded in treated soils. Reduced solubility of Cu and Zn in control soils was related to larger changes in Eh and pH values. Mean comparison with Tukey’s HSD (Honest Significant Difference) test showed that Cu and Zn solubility decreased with decreased Eh and increased pH in the soil solution (p < 0.05%).