An investigation was carried out during 1990-92 at the University Farm, Mohanpur, to study the effect of fertilizer with and without farmyard manure (FYM) on the performance of different wet season rice-based cropping sequences. Rice-wheat or rice-mustard cropping sequence showed greater economic return through the use of FYM at 10 t ha-1 in rice only in conjunction with chemical fertilizer at 100% of the recommended dose. Rice-groundnut cropping sequence showed the highest economic return when only chemical fertilizer was applied. Organic manure plus fertilizer was more beneficial in terms of fertilizer use efficiency and agronomic efficiency of fertilizer use in the rice-wheat and rice-mustard cropping sequences, but this was the reverse in the rice-groundnut sequence. The utilisation of nutrients applied as fertilizer with and without organic manure indicated that cropping sequences significantly enhanced the physiological efficiency and recovery fraction value of fertilizer use.