Sustainable practices in rice cultivation require effective farming management concerning environmental and human health impacts. In this study, three rice cultivation systems, namely low-land, upland, and terraced rice in the Mae Chaem District, Chiang Mai Province, were assessed and the carbon footprint (CF), water footprint (WF), and human and ecotoxicological impacts were compared from pesticide application. The results showed that the highest CF intensity was observed in terraced rice with 1.15 kg CO2eq kg−1 rice yield, followed by lowland rice (1.02 kg CO2eq kg−1 rice yield) and upland rice (0.17 kg CO2eq kg−1 rice yield) fields. Moreover, lowland rice cultivation generated the highest total WF with 1701.6 m3 ton−1, followed by terraced rice (1422.1 m3 ton−1) and upland rice (1283.2 m3 ton−1). The lowland rice fields had the most impact on human health and freshwater ecotoxicity, followed by the terraced and upland rice cultivation systems. The results also showed that most of the pesticides remaining in soils were chlorpyrifos (98.88%), butachlor (96.94%), and fipronil (95.33%), respectively. The substances with the greatest distributions in freshwater were acephate (56.74%), glyphosate (50.90%), and metaldehyde (45.65%), respectively. This study indicated that, with more agricultural inputs, higher CF, WF, human health impacts, and freshwater ecotoxicity were generated. Although the use of pesticides in the study areas did not exceed the recommendations on the packaging, glyphosate and chlorpyrifos are restricted in Thailand, so it is necessary to monitor their use due to their long-term health effects.