Rehabilitated riparian zones in agricultural landscapes enhance environmental integrity and provide environmental services such as carbon (C) sequestration. This study quantified differences in organic matter input, soil biochemical characteristics, and soil respiration in a 25-year-old rehabilitated (RH), grass (GRS), and undisturbed natural forest (UNF) riparian zone. Input from herbaceous vegetation was significantly greater (P < 0.05) in the GRS riparian zone, whereas autumnal litterfall was significantly greater (P < 0.05) in the RH riparian zone. Soil bulk density was significantly greater (P < 0.05) in the RH riparian zone, but its soil chemical characteristics were significantly lower. Soil respiration rates were lowest (P < 0.05) in the UNF (106 C m(-2) h(-1)), followed by the RH (169 mg C m(-2) h(-1)) and GRS (194 C m(-2) h(-1)) riparian zones. Soil respiration rates were significantly different (P < 0.05) among seasons, and were significantly correlated with soil moisture (P < 0.05) and soil temperature (P < 0.05) in all riparian zones. Soil potential microbial activity indicated a significantly different (P < 0.05) response of the microbial metabolic diversity in the RH compared to the GRS and UNF riparian zones, and principle component analysis showed a distinct difference in microbial activity among the riparian land-use systems. Rehabilitating degraded riparian zones with trees rather than GRS is a more effective approach to the long-term mitigation of CO2. Therefore, the protection of existing natural/undisturbed riparian forests in agricultural landscapes is equally important as their rehabilitation with trees, given their higher levels of soil organic C and lower soil respiration rates.