Design and management of the Indus Basin Irrigation System are aimed at achieving equity in canal water supply. This concept, which is more than a century old, ignores the due aspect of groundwater management in today's perspective. Recent research has proved that variation in irrigation demand and rainfall within the irrigation units has given birth to varying stresses on groundwater. In response to spatial climate variability, reallocation of canal supplies from the head towards the tail of the Lower Bari Doab Canal (LBDC) command was evaluated in this study, with the objective of achieving equitable total irrigation costs. The ensuing groundwater regime was simulated for 50 years' time with a groundwater model. A 25% reallocation from head towards tail-end improves the standard deviation of total irrigation cost equity from 1905 to 241. This command scale integration of available water resources also demonstrated a net saving in groundwater pumping cost to the tune of 7.24 to 18.9%, in comparison with existing equitable canal supplies. With this approach, at least minimal or no waterlogging in the head-end area, even during wet years, and no groundwater mining in the tail-end, even during dry periods, are anticipated. In addition, this system-scale integrated water management would increase adaptive capacity to climate change adaptation.