A spatially distributed water‐energy‐food (WEF) nexus model has been developed using the Pardee‐RAND WEF approach to analyse the WEF security of an area. The Pardee‐RAND equations have been modified to include the earlier neglected WEF indicators to tackle the WEF challenges holistically. The model is coded in Python and has an operating system‐independent graphical user interface (GUI). The model helps understand the WEF nexus by calculating water energy, food subindices and the WEF nexus index. We tested the model in the Kangsabati River Basin (distributed at the block level) and across India (states/union territory level). The result shows that the WEF nexus indices vary significantly over the country's small (block) to large (state) administrative units. The water energy and food subindices and WEF nexus index for the Kangsabati River Basin are 0.89, 0.73, 0.79 and 0.80, respectively, while for India, the corresponding values are 0.67, 0.53, 0.73 and 0.63, respectively. The blocks or states/union territories needing specific policy interventions are identified. The study will help influence policy and resource planning at different administrative levels to ensure better management of WEF resources holistically and equitably.