We estimate the nutrient budget in a temporary Mediterranean river basin. We use field monitoring and modelling tools to estimate nutrient sources and transfer in both high and low flow conditions. Inverse modelling by the help of PHREEQC model validated the hypothesis of a losing stream during the dry period. Soil and Water Assessment Tool model captured the water quality of the basin. The 'total daily maximum load' approach is used to estimate the nutrient flux status by flow class, indicating that almost 60% of the river network fails to meet nitrogen criteria and 50% phosphate criteria. We recommend that existing well-documented remediation measures such as reforestation of the riparian area or composting of food process biosolids should be implemented to achieve load reduction in close conjunction with social needs.