This paper focuses on the scope of conjunctive management in the Lower Indus part of the Indus Basin Irrigation System (IBIS), and the contribution this could make towards food security and socio-economic development. The total Gross Command Area (GCA) of the Lower Indus is 5.92 Mha, with a cultivable command area (CCA) of 5.43 Mha, most of which is in Sindh Province. There is a limited use of groundwater in Sindh (about 4.3 Billion Cubic Meter (BCM)) for two reasons: first, there is a large area where groundwater is saline; and second, there is a high surface irrigation supply to most of the canal commands, e.g., average annual supply to rice command is 1723 mm, close to the annual reference crop evapotranspiration for the area, while there is an additional annual rainfall of about 200 mm. These high irrigation allocations, even in areas where groundwater is fresh, create strong disincentives for farmers to use groundwater. Consequently, areas are waterlogged to the extent of 50% and 70% before and after the monsoon, respectively, which contributes to surface salinity through capillary rise. In Sindh, about 74%–80% of the available groundwater recharge is lost in the form of non-beneficial evaporation. This gives rise to low cropping intensities and yields compared to fresh groundwater areas elsewhere in the IBIS. The drought of 1999–2002 has demonstrated a reduction in waterlogging without any corresponding reduction in crop yields. Therefore, in order to efficiently meet current water requirements of all the sectors, i.e., agriculture, domestic and industrial, an ab initio level of water reallocation and efficient water management, with consideration to groundwater quality and its safe yield, in various areas are recommended. This might systematically reduce the waterlogged areas, support greater cropping intensity than is currently being practiced, and free up water for horizontal expansion, such as in the Thar Desert.