Soil available nutrients are very sensitive to change in response to management practices, and are considered to be chemical indicators of soil quality. The present investigation was conducted using two tillage managements for rice (puddled and non-puddled) and wheat (conventional tillage and no-tillage), three water managements and nine nutrient managements. After eight cropping cycles, puddling significantly increased soil organic carbon (SOC) (9.6 g kg(-1)) and available N (159.5 mg kg(-1)) compared to non-puddled soil. The continuous submergence increased the SOC, available Fe, Cu, Mn contents in soil following rice growth, whereas significantly decreased the available N, P and Zn ones. On the contrary, less frequent irrigation improved the SOC, available N and micronutrient contents after wheat cultivation. No-tillage significantly enhanced SOC, available N and Mn. Application of sewage sludge enhanced the soil available Zn (2.98 and 2.09 mg kg(-1)) and Cu (2.95 and 2.06 mg kg(-1)) following harvest of both crops. Organic sources like crop residues, green manure, sewage sludge and combination of organic sources were more effective in improving soil quality indicators.