Nutrients of carbon, nitrogen and water of farmland ecosystem are essential foundation to guarantee crop production, but also environmental flows associated greenhouse gas (GHG), reactive nitrogen (Nr) releases, and water consumption. Their flow characteristics serve as a crucial starting point for creating efficient management practices and mitigation measures. Therefore, the objectives of this study are to quantify the carbon footprint (CF), nitrogen footprint (NF), water footprint (WF), and comprehensive environmental footprint (ComF) of six paddy-upland rotation systems, including fallow-paddy rice (FA-PR), Chinese milk vetch-paddy rice (CMV-PR), wheat-paddy rice (WH-PR), rapeseed-paddy rice (RA-PR), green forage wheat-paddy rice (WF-PR), and vicia faba bean-paddy rice (FB-PR), as well as to analysis their relationships and define driving factors. Results showed that the lowest area-scaled CF of 3.74 t CO2-eq ha−1 were observed in the CMV-PR rotation, which were 41% lower than that for WH-PR (the highest CF, 9.13 t CO2-eq ha−1) when soil carbon change was taken into account. It is of importance that soil carbon sequestration in CMV-PR rotation could offset up to around 57% of its CF, while the WH-PR rotation only offset 25%. The RA-PR rotation had the highest area-scaled NF and WF, which was 1.8 and 1.9 times greater than those of the lowest rotation in FA-PR. In terms of comprehensive environmental effects, the six rotation systems showed the order of FA-PR < CMV-PR < FB-PR < RA-PR < WF-PR < WH-PR, with NH3 volatilization accounting 60.7%–66.7% and blue-green WF for 17.5%–26.6% of the total. Therefore, priority should be given to optimizing N fertilizer application and water consumption for paddy-upland rotation systems. The study also suggested that appropriate inter-annual adjustment of rotation system could contribute to achieving GHG mitigations and Nr losses.
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