The rice (Oryza sativa L.)-wheat(Triticum aestivum L.) cropping system occupies about 24 million ha in Asia and is important for regions food and nutrition security. We analyzed grain yield trends, soil C, apparent nutrient balance (of N,P,K), carbon sequestration, nutrient input use efficiency in a 19 years Long-term rice-wheat experiment conducted at the Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, (22^o58'20''N Latitude and 88^o30'11''E Longitude),West Bengal, India. The 12 treatments were comprised of various combinations of inorganic and organic sources of nutrients. Recommended levels of P and K were used and N levels were supplemented through Farm Yard Manure (FYM), Paddy Straw (PS) and Sesbania (Sesbania aculeata L.) (G.M) in rice (wet season) crop only. Soil parameters were analyzed in archived soil samples collected periodically from 1986 to 2004. Application of NPK and its combination with FYM, PS, GM increased the grain yield of rice and wheat significantly. Rice yield declined only in control plots (T₁= -0.0187) whereas positive yield trend was maintained in all the treatments. Similarly in wheat yield trend was maintained (0.024 Mg ha^-1Yr^-1 to 0.043 Mg ha^-1Yr^-1) over the 19 years in all the treatments. Available N, P and K were increased in all the treatments after 19 cycles of cropping. Available N and P were observed maximum in FYM treatment having 25% substitution (T₇). Organic carbon content was reduced in all the treatments from initial value. However, among the treatments addition of organic inputs like FYM, PS, GM maintained SOC level. Paddy straw and FYM addition caused a greater C sequestration (27.4%, 22.1%) than GM addition (10.3%). The low C/N ratio of green manure resulted in lower amounts of C sequestration. The apparent N and P balance showed positive except in control treatment over the years, whereas apparent K balance showed net losses of K ranging from –11.6 to –100.0 kg ha^-1yr^-1. In spite of heavy with drawl of K yield trend of both rice and wheat was maintained due to build up of N and P from various organic inputs. Partial factor productivity (PFP_N) for Nitrogen was much higher ranging from 45.2 to 47.8 (T₆ - T₁₁) than T₅ (43.5) in rice and that of wheat ranged form 31.3 to 39.1 (T₆ to T₁₁) than 29.0(T₅). Agronomic efficiency (AE_N) ranged between 26.9 to 38.5 in rice and 17.9 to 25.9 in wheat. The higher vales of AE_N in rice indicating direct effect of FYM, PS and GM than residual effect in succeeding wheat crop. Recovery efficiency (RE_N) values ranged between 0.16 to 0.44 in rice and 0.18 to 0.40 in wheat. Sustainability Yield Index (SYI) varied from 0.54 to 0.70% for rice and 0.35 to 0.67 % in wheat. Micronutrient depletion was noticed after 19 cycles of cropping. It is possible to sustain high yields if fertilizer regimes are updated regularly to maintain the congruence between crop N, K demand and the N, K supply from soil, manures and fertilizers.