A comparison was made between a long-term rice–wheat cultivation with fertilizer nitrogen–phosphorus–potassium (NPK) or added organics [farmyard manure (FYM), paddy straw (PS), green manure (GM)] and a permanent fallow on bulk density (BD), saturated hydraulic conductivity (Ksat), available water capacity (AWC), maximum water-holding capacity (MWHC), aggregation, and soil organic carbon (SOC) dynamics on an Inceptisol of humid subtropics of eastern India. Continuous cropping caused a net decrease in SOC content. Undisturbed fallow was comparable to soils with FYM, PS, and GM amendments in structural and hydrophysical properties. Maximum WHC and AWC values were in the order of FYM followed by PS, GM, fallow, NPK, and control. The relative efficacy of the organics for physical buildup was FYM > PS > GM, which increased structural indices. This study represents further steps toward understanding the ecological importance of fallow management and integrated use of balanced fertilizer and organics.