Background: Biochar is a promising material in mitigating greenhouse gases (GHGs) emissions from paddy fields due to its remarkable structural properties. Rice husk biochar (RhB) and melaleuca biochar (MB) are amendment materials that could be used to potentially reduce emissions in the Vietnamese Mekong Delta (VMD). However, their effects on CH4 and N2O emissions and soil under local water management and conventional rice cultivation have not been thoroughly investigated. Methods: We conducted a field experiment using biochar additions to the topsoil layer (0-20 cm). Five treatments comprising 0 t ha-1 (CT0); 5 t ha-1 (RhB5) and 10 t ha-1 (RhB10), and 5 t ha-1 (MB5) and 10 t ha-1 (MB10) were designed plot-by-plot (20 m2) in triplicates. Results: The results showed that biochar application from 5 to 10 t ha-1 significantly decreased cumulative CH4 (24.2-28.0%, RhB; 22.0-14.1%, MB) and N2O (25.6-41.0%, RhB; 38.4–56.4%, MB) fluxes without a reduction in grain yield. Increasing the biochar application rate further did not decrease significantly total CH4 and N2O fluxes but was seen to significantly reduce the global warming potential (GWP) and yield-scale GWP in the RhB treatments. Biochar application improved soil Eh but had no effects on soil pH. Whereas CH4 flux correlated negatively with soil Eh (P < 0.001; r2 = 0.552, RhB; P < 0.001; r2 = 0.502, MB). Ameliorating soil aeration and functions by adding RhB and MB resulted in improving soil physicochemical properties, especially significant SOM and AN boosting, which indicate better soil health, structure, and fertility. Conclusions: Biochar supplementation significantly reduced CH4 and N2O fluxes and improved soil mineralization and physicochemical properties toward beneficial for rice plants. The results suggest that the optimal combination of biochar-application rates and effective water-irrigation techniques for soil types in the MD should be further studied in future works.