Output:input ratios and apparent balances for nitrogen (N), phosphorus (P) and potassium (K) were measured in a rice-wheat system at Modipuram (29.4°N, 77.46°E, 237 m asl), India, under two planting densities (P1 = 200×200 mm for rice, 230 mm row spacing for wheat, and P2 = 200×100 mm for rice, 150 mm row spacing for wheat), and two levels of fertilizer NPK (100% F = recommended levels of fertilizer N, P and K for each crop, i.e. 120 kg N, 26 kg P and 33 kg K ha−1, and 150% F = 150% of the recommended levels) with and without 5 t ha−1 farmyard manure (M) to each crop. After two cycles of the rice-wheat rotation at a fixed site, N and K balances were negative for all treatments, but P balance was negative only in plots treated with P1 + 100% F treatment. The largest yield in the system, 15.7 t ha−1, was obtained in plots receiving P2 planting density with 150% F + M treatment, and the smallest (13 t ha−1) in plots of P1 planting density with 100% F treatment. In plots with the largest yield, total removal of NPK was 659 kg ha−1 (310 kg N, 62 kg P and 287 kg K ha−1), and in plots with the smallest yield, NPK removal was 411 kg ha−1 (188 kg N, 34 kg P and 189 kg K ha−1). At these nutrient uptakes, output:input ratios were 0.74 for N, 0.57 for P and 1.80 for K in plots receiving P2 + 150% F + M treatment, and 0.78 for N, 0.65 for P and 2.86 for K in plots receiving P1 + 100% F treatment.