The repository includes the research data pertaining to the Modflow-NWT based groundwater model developed for the Koga irrigation project area, Ethiopia. The database constitutes three archived data folders namely, 1. MainData (mostly excel files which include model forcings, data used in model calibration, citizen science data, etc.), 2. GIS (mostly geospatial files to assist readers with the spatial locations of the irrigation project structures, as well as the important data and administrative locations), 3. ModelFiles (mostly text files which include model inputs and outputs). The data has been used in preparation of the manuscript titled, "A numerical framework to advance agricultural water management under hydrological stress conditions in a data scarce environment", published in the Agricultural Water Management journal (10.1016/j.agwat.2021.106947). Readers are requested to go through this article to find more details on the data. The model simulations ranged from 1st January 2008 to 15th August 2019.