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In south Asian countries, production fatigue has been observed as yields which have started declining or stagnating under long-term experiments in multiple cropping systems due to continuous cultivation. We examined the potential impact of continuous cultivation of crops in rotation, and fertilizer and manure application on yield trends, soil organic carbon (SOC) storage, soil quality parameters (active fractions of SOC in particular) and sustainable yield index (SYI). Crop rotations included in the study were: rice-wheat-jute, soybean-wheat and sorghum-wheat system at Barrackpore (Typic Eutrochrept), Ranchi (Typic Haplustalf) and Akola (Typic Haplustert), respectively. Field treatments included unfertilized (control), 100% N, 100% NP, 100% NPK and 100% NPK + FYM. The negative yield trend was observed in unbalanced use of inorganic N and NP application at all the three sites. The positive yield trend was observed in the NPK and NPK + FYM treatments at Ranchi and Akola. However, significantly negative-yield trends were observed in these treatments at Barrackpore under rice-based system. Results showed that the SOC in the unfertilized plot (control) decreased by 41.5, 24.5, and 15.5% compared to initial values in Barrackpore, Ranchi and Akola, respectively, wherein the treatment receiving NPK and NPK + FYM either maintained or improved it over initial SOC content in these sites. The estimated annual C input values in NPK + FYM treatments were 4392, 4159 and 3113 kg ha(-1) year(-1) in rice-wheat-jute, sorghum-wheat and soybean-wheat system, respectively. Active fractions of SOC, viz., water-soluble carbon and hydrolysable carbohydrates, soil microbial biomass C and N, dehydrogenase and alkaline phosphatase activity, improved significantly with the application of NPK and NPK + FYM. The content of SOC significantly (p <= 0.05) correlated with SYI and active fractions of SOC, which support better sustainable productivity. Results suggest that current fertilizer recommendations of 100% recommended NPK are adequate for maintaining SOC and its active fractions as well. The causes of yield decline are mostly location specific but depletion of SOC and its active fractions seems to be a general cause. (c) 2004 Elsevier B.V. All rights reserved.