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The present study analyzed the effect of different organic and inorganic fertilizers on soil nutrient dynamics in a long-term field experiment under rainfed rice-lentil system. The experiment was operative at Agricultural Research Farm, Institute of Agricultural Sciences, B.H.U Varanasi, Uttar Pradesh, India. Carbon dynamics was investigated on surface soil on the basis of distribution of Walkley & Black Carbon, in active pool (AP) or labile carbon (oxidisable at low concentration of H2SO4) in relation to passive pool (PP) or non labile carbon (oxidisable at high concentration of H2SO4) and its indices carbon management index (CMI). The effect of eight different treatments including unfertilized, 100% N from farm yard manure, 100% recommended dose of fertilizer, 50% RDF + 50% N Foliar), 50% RDF, 50% RDF + 50% N FYM), 50% N FYM and Farmers practices i.e. application of 20kg N ha-1 The availability & uptake of major nutrients were studied. The results revealed: That mixed application of inorganic fertilizers and FYM substantially increase the soil organic carbon pool, sustainability index over remaining treatments. Higher fertilizer application rates resulted in higher and sustained crop yields which had been reflected in sustainability yield index. A significant Pearson correlation was found between SOC, AP, PP, exchangeable K2O content, soil microbial biomass carbon and SYI. (The result indicated to adopt conjunctive use of nutrient management which promote the SOC more labile and, induce availability of other nutrients coupled with SMBC that translate into higher crop yields.