The effectiveness and productivity of Regadio irrigation systems and water management techniques in Portugal’s Cova da Beira region are assessed in this study. Maintaining agricultural activity and resolving the region’s water scarcity issues depend heavily on the Regadio system. The research finds areas for improvement and suggests methods to increase the irrigation system’s productivity, efficiency, and sustainable water use by examining the current infrastructure and management practices. This study used 7 years of observations (2016–2022) to evaluate system performance, drawing on a comprehensive dataset spanning the operating points of the “Regadio” system—specifically, Belmonte, Covilhã, Fundão, Penamacor, and Sabugal. To evaluate the impacts of farm size—differentiating between smaller holdings (less than 20 ha) and larger ones (more than 20 ha)—on irrigation system performance, as indicated by the ratio of irrigated area to benefitted area, the analysis uses panel data and quantile regression techniques. The findings show that the size of agricultural holdings has a major impact on how well the irrigation system works, with larger units having a beneficial effect on efficiency. Regional economic returns have a significant and favorable impact on system performance, according to the panel data study. However, in the quantile regression, where environmental threats have a more noticeable detrimental influence, this effect is not verified. These results highlight the significance of contextual and structural elements in determining the sustainability and efficacy of irrigation systems in a certain spatial area.