Soil salinity is the major constraint for cropping system intensification in the coastal region of the Ganges Delta. Salts build up on the soil surface, as well as in the crop root zone, due to the capillary rise in underground brackish water, hampering the growth and development of crops and resulting in mortality and low yields. We studied, for three years (2020–2021 to 2022–2023), the effect of conservation agricultural practices (zero tillage planting, crop residue recycling, and crop rotations) on the major soil properties (soil salinity and organic carbon status), crop performance (yield and economics), and water footprint. Conservation agricultural practices significantly reduce soil salinity, build soil organic carbon, reduce water footprint, and increase the profitability of cropping systems compared to tillage-intensive conventional practices. Under conventional agriculture, the sole cropping of rice is more profitable than double and triple cropping systems.