Detecting Hidden Environmental Flow Alteration in Groundwater‐Irrigated Basins

ABSTRACT Effective and balanced management of economic and environmental concerns in groundwater‐irrigated basins is a world‐wide challenge. Environmental flow modification is increasingly influenced by groundwater‐supported irrigation in these heavily irrigated regions, yet the ability to rigorously quantify how groundwater‐based irrigation influences ecological surface‐water flows remains limited, leaving resource managers with difficult and opaque decisions regarding resource allocation. This work presents a generic and generalised framework to programmatically evaluate how groundwater use for irrigation has altered surface‐water flow characteristics by using an integrated surface‐subsurface modelling system paired with rigorous ensemble‐based data assimilation. As an example, we demonstrate the mechanisms linking groundwater dynamics to environmental flow alteration in groundwater‐dependent river systems, utilising the Mississippi Alluvial Plain (MAP), USA, as a representative study. Specifically, a coupled SWAT+ gwflow model was applied across six HUC‐8 watersheds and calibrated using an iterative ensemble smoother, incorporating both monthly streamflow and groundwater head observations. Model performance was evaluated using multiple hydrologic metrics and independent datasets, including streamflow, groundwater levels and basin‐scale evapotranspiration. Environmental flow alteration was quantified using the IAHRIS framework under managed and naturalised conditions. Results reveal that while annual discharge volumes remain near stable, substantial degradation occurs in low‐flow magnitude, duration and seasonal structure. Groundwater abstraction‐induced baseflow reduction emerged as the primary driver of low‐flow collapse, particularly during the irrigation season. The proposed framework provides a transferable, process‐oriented methodology for diagnosing groundwater‐driven environmental flow alteration in intensively irrigated basins and offers a robust basis for evaluating sustainable groundwater–surface water management strategies under increasing water demand.