In most cases, intermittent rivers and ephemeral streams (IRES) form the principal surface water bodies in Mediterranean regions and people are heavily dependent on them. Strong reliance on such streams results in numerous pressures, and complex relationships are formed between their various natural and anthropogenic components, which creates numerous challenges to decision-makers who require a better understanding of IRES to establish effective measures to restore ecosystem functionality and implement changes, while maintaining human well-being. In this paper, we present a conceptual framework that identifies process cascades and links to identify the variables governing Mediterranean IRES and map their complex interrelations.Climate is the main external driver, and it affects IRES through precipitation, temperature, wind action, and geomorphic factors, which in turn influence the physical and biological attributes of IRES. Monitoring challenges and knowledge gaps are presented from the conceptual framework, highlighting the need to identify solutions for the monitoring and mapping the spatio-temporal variability of flow regimes and their influence on bio-physical variables and mapping and quantifying ecosystem services for integrated environmental management. Finally, we argue that remote sensing techniques, specifically, the combined use of unmanned aerial vehicles and structure from motion photogrammetry, are key to bridging gaps in understanding and meeting the challenges of managing Mediterranean IRES.