Globally South Asia, where agriculture plays a key role in the economy, has been identified as the second lowest in terms of regional level food security. National- and Regional scale research and development activities are important in improving the agriculture and food security of the region. Sea level rise due to climate change has affected the low-lying agricultural areas of South Asia. In addition, various anthropogenic activities leading to salt water intrusion have worsened the situation. In addressing climate change related issues, both mitigation of greenhouse gas (GHG.) emissions and adopting appropriate adaptation measures to minimize the impacts are necessary. Remedial measures to alleviate soil salinity include addition of organic manure and management of stagnant water. In addressing the salinity issue, remedial measures adopted on salt-affected soils to reduce the salinity effect could enhance future climate change if they cause high levels of net GHG emissions. Therefore this study addresses the best agricultural management practices for salt-affected soils in rice cropping systems of the South Asian region considering net GHG emissions and other socioeconomic benefits associated with the adopted measures. Country-level studies so far have mostly shown the impact of the remedial measures on paddy yields and soil quality. The outcome of this collaborative project will be used to raise awareness among farmers for adopting climate-friendly best management practices for salt-affected soils and make recommendations in developing adaptation policies and strategies within the respective countries and the region as a whole.