Natural farming (NF) has emerged as a promising agro-ecological tactic to enhance resource use and reduce dependence on synthetic agricultural inputs. However, comprehensive field-based evidence across diverse agro-climatic regions remains limited. This study assessed the effects of NF on water use, water and crop productivity, economic returns, energy consumption, and soil fertility across four agro-climatic zones of Andhra Pradesh, India, using a paired-field approach during 2023–2025. Compared with conventional farming (CF), NF reduced total water utilization by 16.1–39.0%, resulting in a 15.0–55.5% improvement in water productivity. Although rice yield declined marginally by 4.40–8.40% in the Southern, Krishna, and High-Altitude zones during some seasons, yields remained comparable in the Godavari zone. The cost of cultivation decreased substantially by 20.6–35.1%, while gross returns remained largely comparable between production systems, varying from −7.0% to +5.05%. Consequently, NF increased net returns by 8.8–29.0% and improved the benefit-cost ratio by 23.7–47.8% relative to CF. Irrigation-related energy consumption was reduced by 21.8–57.7%, indicating greater resource-use efficiency under NF. The sustainable yield index values remained high (0.68–0.91), demonstrating stable crop productivity despite reduced external inputs. Natural farming practices also improved soil health by buffering soil pH towards neutrality; soil organic carbon (SOC) enhanced from 0.38–0.73% under CF to 0.57–1.01% under NF. Similarly, available nitrogen, phosphorus, and potassium increased under NF. Overall, these findings demonstrate that natural farming improves water and energy productivity, reduces production costs, and increases farm profitability while maintaining stable rice productivity across diverse agro-climatic conditions. The results highlight the potential of natural farming as a climate-resilient and resource-efficient strategy for sustainable rice production in India.