Coastal back-barrier perched lakes are freshwater bodies that are elevated over sea-level and are not directly subjected to the inflow of sea-water. This study provides a detailed reconstruction of the Doniños back-barrier perched lake that developed at the end of a small river valley in the rocky coast of the northwest Iberian Peninsula during the Holocene transgression. Its sequence stratigraphy was reconstructed based on a core transect across the system, the analyses of its lithofacies and microfossil assemblages, and a high-resolution radiocarbon-based chronology. The Doniños perched lake was formed ca. 4.5 ka BP. The setting of the perched lake was favoured by Late Holocene sea-level stabilization and the formation of a barrier and back-barrier basin, which was contemporaneous with the high systems tract period. This basin developed over marine and lagoonal sediments deposited between 10.2 and 8.0 ka BP, during rapidly rising sea-level characteristic of the transgressive systems track period. At 1.1 ka BP, the barrier was breached and the perched lake was partially emptied, causing the erosion of the back-barrier basin sediments and a significant sedimentary hiatus. Both enhanced storminess and human intervention were likely responsible for this event. After 1 ka BP, the barrier reclosed and the present-day lake was reformed, with the water level reaching as high as 5 m amsl. The depositional evolution of the Doniños system serves as a model of coastal back-barrier perched lakes in coastal clastic systems that have developed over gently seaward-dipping rugged substrates at small distances from the shoreline and under conditions of rising sea-level and high sediment supply. A review of estuaries, back-barrier lagoons, pocket beaches and back-barrier perched lakes in the rocky coast of the northwest Spain shows that the elevation of the bedrock is the main factor controlling the origin and evolution of these systems.