Carbon sequestration on soil is one of the counter measurements against climate change in agricultural sector. Increasing incorporation of organic fertilizer would increase soil organic carbon (SOC) but it could bring high potential of nutrient losses which would result in water quality degradation. In this paper, literature review on soil organic carbon behavior according to agricultural management is presented. The results of field experiment to identify the effect of organic and commercial fertilizer applications on SOC and runoff water quality were also presented. Field experiment confirmed increased SOC and nutrient concentrations in runoff water as application rate of organic fertilizer increase. The potential use of simulation model to develop best agricultural management practice considering carbon sequestration and water quality conservation at the same time is discussed and monitoring and modeling strategies are also suggested to achieve the goal.