Ecological integrity is fundamental to human life and ecosystems, so its assessment and management are crucial. This concept assesses ecosystem health by examining physico-chemical and biological characteristics, riparian vegetation and macroinvertebrate communities. In recent decades, water resources have undergone significant changes due to various factors that have contributed to the physical, chemical and biological pollution of water. To address this problem, a specific model has been developed using the Partial Least Squares Path Modelling methodology to analyse and quantify the main factors affecting the ecological integrity of the Spanish part of the Guadiana River (Spain). The variables analysed at the different sampling points in the catchment include forest cover, anthropogenic pressure, water quality and biological integrity. Water quality and biological integrity, in turn, constitute the concept of ecological integrity. The model predicts 60.3 % of the physico-chemical water quality and 56.6 % of the biological integrity, showing that ¨Forest cover¨ negatively impacts water quality (W = −0.476) by reducing pollution, while ¨Anthropogenic Pressure¨ positively impacts it (W = 0.680) by increasing pollution. Based on the modelling, three future scenarios were designed, from the lowest to the highest pressure considering changes in riparian forest quality based on QBR and changes in the number of reservoirs: a favourable scenario with high riparian forest quality and no reservoirs; an intermediate scenario with good riparian forest quality and no change in the number of reservoirs; and an unfavourable scenario, characterised by very poor riparian forest quality and an increase in the number of reservoirs. In this context, the importance of the conservation and enhancement of riparian vegetation as a nature-based solution is highlighted, as well as the pressure generated by industrial activity and agricultural practices on the ecological integrity of the study area. The favourable scenario, with very good quality riparian vegetation, improves water quality by up to 85 %, positively impacting the ecological integrity of the river. In contrast, the unfavourable scenario, with extremely degraded riparian forest, would decrease water quality by up to 62 %, negatively affecting ecological integrity. Modelling and future scenarios is an essential tool in the decision-making process to improve environmental governance and water security. In addition, the PLS-PM methodology allows the identification and quantification of relationships between complex variables, providing a solid basis for the design of effective environmental management strategies.