River basin modeling under complexity requires analytical frameworks capable of dealing with the multiple scales and dimensions of environmental problems as well as uncertainty in the evolution of social systems. Conceptual and methodological developments can now be framed using the wide socio-eco-hydrological approach. We add hierarchy theory into the mix to discuss the conceptualization of river basins as complex, holarchic social-ecological systems. We operationalize the social-ecological systems water metabolism framework in a semiarid watershed in Spain, and add the governance dimension that shapes human-environment reciprocity. To this purpose, we integrate an eco-hydrological model with the societal metabolism accounting scheme for land use, human activity, and water use. We explore four types of interactions: between societal organization and water uses/demands, between ecosystem organization and their water requirements/supplies, between societal metabolism and aquatic ecosystem health, and between water demand and availability. Our results reveal a metabolic pattern of a high mountain rural system striving to face exodus and agricultural land abandonment with a multifunctional economy. Centuries of social ecological evolution shaping waterscapes through traditional water management practices have influenced the eco-hydrological functioning of the basin, enabling adaptation to aridity. We founda marked spatial gradient on water supply, use pattern, and impact on water bodies from the head to the mouth of the basin. Management challenges posed by the European water regulatory framework as a new driver of social-ecological change are highlighted.