While previous studies have suggested that biochar, nitrification inhibitors, and urease inhibitors may reduce soil greenhouse gas emissions, their effectiveness in soils irrigated with alternative water resources remains unclear. To compensate for this, reclaimed water and livestock wastewater were utilized as alternative water resources alongside groundwater control. Nitrapyrin and N-(n-butyl) thiophosphoric triamide and biochar were applied to the soil either individually or in combination, and a no-substance treatment (NS) was included for comparison. The results revealed that reclaimed water and livestock wastewater irrigation exacerbated the global warming potential. Compared to the NS, all exogenous substance treatments suppressed nitrous oxide (N₂O) emissions while increasing carbon dioxide (CO₂) emissions, and affecting methane (CH₄) emissions varied across treatments irrespective of the water types. Interestingly, the additional biochar reduced the inhibitory effect of the inhibitors on the greenhouse effect. Using nitrification inhibitors reduced the global warming potential by 48.3% and 50.1% under reclaimed water and livestock wastewater irrigation, respectively. However, when nitrification inhibitors were applied in combination with biochar, the global warming potential was increased by 52.1–83.4% compared to nitrification inhibitors alone, and a similar trend was also observed in the scenario of urease inhibitors, with increases ranging from 8.8 to 35.1%. Therefore, the combined application of biochar and inhibitors should be approached cautiously, considering the potential for increased greenhouse gas emissions.