Soil organic C (SOC) pools under long-term management practices provide information on C sequestration pathways, soil quality maintenance, and crop productivity. Farmyard manure (FYM), paddy straw (PS), and green manure (GM) along with inorganic fertilizers were used in a 19-yr-old rice (Oryza sativa L.)-wheat (Triticum aestivum L.) cropping system in subtropical India to evaluate their impact on SOC stock, its different pools-total organic C (C-tot); oxidizable organic C (C-oc) and its four fractions of very labile (C-frac1), labile (C-frac2), less labile (C-frac3), and nonlabile C (C-frac4); microbial biomass C (C-mic); and mineralizable C (C-min). Cropping with only N-P-K fertilization just maintained SOC content, while N-P-K plus organics increased SOC by 24.3% over the control, their relative efficacy being FYM > PS > GM. A minimum of 3.56 Mg C ha(-1) yr(-1) was required to be added as organic amendments to compensate for SOC loss from cropping. The passive (C-frac3 + C-frac4) pool and C-min constituted about 39 and 11.5%, respectively; of C-tot. Organics contributed toward the passive pool in the order FYM > PS > GM. Most of the pools were significantly (P = 0.005) correlated with each other. Yield and sustainable yield index were strongly related with C-frac1, C-oc, C-mic, and C-min. Results suggest C-frac1 as a useful indicator for assessing soil health, and balanced fertilization with FYM as suitable management for sustaining crop productivity of the rice-wheat system.