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Since reckonable understanding of yield response under long-term (16 year) conservation management practices is the key to improve the productivity and physico-chemical indicators of rice-wheat rotation, impact of long-term tillage and irrigation levels on productivity, yield trend, soil organic carbon (SOC) fractions, carbon pools and sequestration under rice-wheat rotation on sandy clay loam soil of the mid-Himalaya were quantified. A field experiment started from 2001 through 2016 to assess the effect of tillage alterations conventional tillage (CT) and zero tillage (ZT) and four irrigation levels I1: pre-sowing (PS), I2: PS + crown root initiation (CRI), I3: PS + CRI + panicle initiation (PI)/flowering (FL), and I4: PS + CRI + PI/FL + grain filling (GF), applied at the critical growth stages to rice-wheat rotation. Results confirmed that irrigation management had a significant (p = 0.001) positive impact on grain yield of rice, wheat and system yield after 16 year continuous cropping. We also recoded that, plot with four irrigation (I4) had ∼ 28, 40 and 35 % higher grain yield of rice, wheat as compared to single irrigation or I1 (2.04, 2.99 and 5.05 Mg ha−1), respectively. Rice yield declined significantly (r = 0.68; p = 0.003) by 70 kg ha−1 year−1 under ZT plots than CT plots (52 kg ha−1 year−1). Decreasing trend of rice yield ranged from 42 kg ha−1 year-1 in four irrigations (I4) to 75 kg ha−1 year−1 single irrigation (I1). Whereas, wheat yield increased (58 kg ha−1 year−1) non-significantly over the years under ZT plots whereas under CT plots (-13.6 kg ha−1 year−1) it had declining trend with time. Unlike rice yield, impact of irrigation on wheat yield had positive trends or increasing trends with time. Plots under long-term ZT along with irrigation practice significantly increased total porosity and decreased pH and bulk density (BD) mainly in surface layer. Different pools of SOC were also significantly increased under ZT as compared to CT only in surface layer (0−15 cm). We conclude that, ZT system increased yield of wheat and diminished rice yield after 16 years of experimentation. But apart from yield, ZT also improved physico-chemical indicators of soil and enhanced carbon sequestration. The WUE of rice and wheat (4.20 and 11.0 kg ha−1 mm−1) had slightly higher under ZT as compared to CT. It is suggested that ZT is more desirable for efficient water utilization in such conditions. Frequent irrigation (I4) was more desirable for maintaining optimum moisture condition for sustainable crop production.