This paper analyses the effects of environmental flows on water quality within a highly regulated basin, focusing on the Turia River basin in the eastern Iberian Peninsula. Through water management and water quality models, a series of simulations were conducted, introducing variations in the outflows of the Loriguilla reservoir to evaluate the effects of different environmental flow scenarios on water quality, particularly at the location of the intake for the water supply to Valencia. Three environmental flow scenarios were analyzed, alongside an alternative management scenario, considering their implications on water quality and reliability of water demand. The findings of this paper, particularly the nitrate (NO3−) concentration evolution, highlight the influence of minimum e-flow and e-flow regimes on water quality within the basin. These results suggest that while modifying the current flow regime can lead to some improvements in nitrate concentrations at the Valencia supply intake point, the primary cause of high nitrate concentrations is attributed to irrigation return flow and the pre-existing contamination of the aquifer. This analysis offers valuable insights into the complexities of water quality management in regulated basins, emphasizing the need for a multi-faceted approach to address the diverse factors influencing water quality and demand supply reliability.