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Intensive tillage based management practices are threatening soil quality and systems sustainability in the rice-wheat belt of Northwest India. Furthermore, it is accentuated with puddling of soil, which disrupts soil aggregates. Conservation agriculture (CA) practices involving zero tillage, crop residue management and suitable crop rotation can serve as better alternative to conventional agriculture for maintaining soil quality. Soil organic carbon is an important determinant of soil quality, playing critical role in food production, mitigation and adaptation to climate change as well as performs many ecosystem functions. To understand the turnover of soil carbon in different forms (Total organic carbon-TOC; aggregate associated carbon-AAC; particulate organic carbon-POC), soil aggregation and crop productivity with different management practices, one conventional agriculture based scenario and three CA based crop management scenarios namely conventional rice-wheat system (Sc1), partial CA based rice-wheat-mungbean system (Sc2), full CA-based rice-wheat-mungbean system (Sc3) and maize-wheat-mungbean system (Sc4) were evaluated. TOC was increased by 71%, 68% and 25% after 4 years of the experiment and 75%, 80% and 38% after 6 years of the experiment in Sc4, Sc3 and Sc2, respectively, over Sc1 at 0-15 cm soil depth. After 4 years of the experiment, 38.5% and 5.0% and after 6 years 50.8% and 24.4% improvement in total water stable aggregates at 0-15 and 15-30 cm soil depth, respectively was observed in CA-based scenarios over Sc1. Higher aggregate indices were associated with Sc3 at 0-15 cm soil depth than others. Among the size classes of aggregates, highest aggregate associated C (8.94 g kg(-1)) was retained in the 1-0.5 mm size class under CA-based scenarios. After 6 years, higher POC was associated with Sc4 (116%). CA-based rice/maize system (Sc3 and Sc4) showed higher productivity than Sc1. Therefore, CA could be a potential management practice in rice-wheat cropping system of Northwest India to improve the soil carbon pools through maintaining soil aggregation and productivity.