Rice-based multiple cropping systems are predominant in the Indo-Gangetic Plains of Indian subcontinent. A decline in yield of such systems has been observed and ascribed to quantitative and qualitative variations of soil organic matter (SOM). We evaluated the impact of the annual rotation: rice (Oryza sativa L.), wheat (Triticum aestivum L.), jute (Corchorus olitorius L.), with and without fertilizer treatments (control, N, N-P, N-P-K, and N-P-K plus farmyard manure FYM) on SOM and aggregate properties. At 0- to 15-cm soil depth, microbial biomass C and N, hot water-soluble C and N and hydrolyzable carbohydrates, and particulate organic matter C (POMC) and N (POMN) were found in the order N-P-K plus FYM > N-P-K > N-P > N > control. Over the course of the experiment, application of N alone decreased total organic C (TOC) by 20.4%, whereas N-P-K with or without FYM addition either maintained or enhanced compared to initial. Total soil N and mineralizable N declined in all the treatments except N-P-K plus FYM. Irrespective of treatments, microaggregates (53-250 micrometer) dominated with 43.9 to 51.3% of total soil aggregate size distribution, followed by macroaggregates (250-2000 micrometer with 34.6 to 40.1%). The C and N mineralization rate was greater in macroaggregates than in microaggregates, and correlated significantly with POMC (r = 0.67, P less than or equal to 0.01) and POMN (r = 0.88, P less than or equal to 0.01). Nitrogen-phosphorus-potassium plus FYM also improved overall soil aggregation as compared to other treatments. Therefore, the results suggest that the gradual depletion of nutrients and structural degradation may have collectively contributed to the crop yield declines in the rice-wheat-jute rotation and that the integrated use of N-P-K and FYM is an important nutrient management option for sustaining this cropping system.