The cultivation of rice is one of the main sources of greenhouse gas (GHG) emissions due to continuously flooded irrigation (CF), which demands large volumes of water. As an alternative solution, alternate wetting and drying (AWD) irrigation has been developed as a water-saving strategy. This study was conducted at the Experimental Agricultural Station (EEA) in Vista, Florida, in the Lambayeque region located on the northern coast of Peru. Thus, it was analyzed the effect of AWD irrigation at different depths (5, 10, and less than 20 cm below the surface) compared to CF control on methane (CH4) and nitrous oxide (N2O) emissions and rice grain yield. AWD treatments reduced CH4 emissions by 84% to 99% but increased N2O emissions by 66% to 273%. In terms of Global Warming Potential (GWP), the AWD10 treatment demonstrated a 77% reduction and a Water Use Efficiency (WUE) of 0.96, affecting only a 2% decrease in rice grain yield, which ranged between 11.85 and 14.01 t ha−1. Likewise, this study provides sufficient evidence for the adoption of AWD irrigation as a strategy for the efficient use of water resources and the mitigation of GHG emissions in rice cultivation in the study area, compared to continuous flooded irrigation.