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Tamil Nadu in particular is a key rice-producing region in peninsular India. Hydrochemistry, viz., redox potential (Rh), soil temperature and dissolved oxygen (DO), of rice soils can determine the production of greenhouse gas methane (CH₄). In recent decades, the cultivation of crops organically became a viable option for mitigating climate change. Hence, this study aimed to investigate the effects of different organic amendments on CH₄ emission, Rh, DO, and soil and water temperature (T) in relation to the yield of paddy. The treatments composed of viz., control, blue-green algae (BGA), <i>Azolla</i>, farm yard manure (FYM), green leaf manure (GLM), blue-green algae + <i>Azolla</i>, FYM + GLM, BGA + <i>Azolla</i> + FYM + GLM, vermicompost and decomposed livestock manure. With the addition of BGA + <i>Azolla</i>, the highest reduction in CH₄ emission was 37.9% over the control followed by BGA. However, the same treatment had a 50% and 43% increase in Rh and DO, respectively, over the control. Established Pearson correlation analyses showed that the CH₄ emission had a positive correlation with soil (r = 0.880 **) and water T (r = 0.888 **) and negative correlations with Rh (r = −0.987 **) and DO (r = −0.963 **). The higher grain yield of 26.5% was associated with BGA + <i>Azolla</i> + FYM + GLM application. Our findings showed that there are significant differences in CH₄ emissions between different organic amendments and that hydro-parameters may be a more important controlling factor for methane emissions than temperature. The conclusion has been drawn based on valid research findings that bio-fertilization using BGA and <i>Azolla</i> is an efficient and feasible approach to combat climate change, as it assists in reducing methane emissions while simultaneously boosting crop yield by fixing nitrogen into the soil in the studied agro-climatic zone.