Heavily modified water bodies (HMWB) have been seriously affected by human activities and natural processes promoting their imbalance, and impacting their functioning and biodiversity. This study explores a new approach of monitoring and assessing water quality in Mediterranean reservoirs using phytoplankton communities across a disturbance gradient, according to water framework directive. Phytoplankton and environmental data were sampled in 34 reservoirs over 8 years. Two types of reservoirs were analyzed: Type1 “run-of-river reservoirs” (located in the main rivers, with a low residence time); and Type2 “true reservoirs” (located in tributaries, with high residence time). The transition from deeper and colder reservoirs (reference sites) to shallow and warmer (impaired sites) was clear in Type2, correlated to organic pollution and mineral gradients. Impaired sites from both types showed a higher richness of tolerant taxa. Principal response curve (PRC) provided a concise summary of phytoplankton temporal dynamics and assessed ecosystem health for Mediterranean HMWBs. PRC will provide a powerful tool for environmental quality assessment and be incorporated into monitoring and assessment programs. This approach can help policymakers to manage natural capital to achieve multiple objectives, mainly increasing ecosystem services, and improve readability and interpretation of spatial patterns in temporal changes.