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A profound consideration of soil organic carbon (SOC) and SOC pools as affected by the long-term use of fertilizer in a fixed crop sequence is essential to understand and maintain the health and productivity of soil. The dynamics of SOC pools, i.e. total soil organic carbon (TOC) and its different fractions under a rice-wheat cropping system subjected to various fertilizer management strategies over 42 years was investigated near Uttarakhand, India. The soil at the experimental site was an Aquic Hapludoll consisting of a poorly drained silty clay loam (1–1.5 m deep) overlying loamy to sandy sediments. Over 42 years, application of 100% NPK+ FYM (Farm Yard Manure) was the most effective management system in increasing organic C up to 0 to 60 cm soil depths under rice-wheat sequence. The combination of this integrated input application (100% NPK + 15 t ha−1 FYM) significantly built organic carbon fractions like total organic carbon, microbial biomass C (MBC), particulate organic C (POC), KMnO4 oxidizable C, Humic C, Fulvic C, Humin C, water-soluble carbon and hot water extractable carbohydrates at all four soil depths. Hence, application of FYM along with NPK resulted in a significant positive building up of all pools in the treatment at all four depths. Therefore, balance fertilization is panaceally important for sustaining improved soil health with balanced organic status and production potentiality of the soil for rice-wheat cropping sequence. [ABSTRACT FROM AUTHOR]