The foraminiferal assemblages recorded in the modern environment and sedimentary successions of two boreholes drilled in the Melides lagoon have been analyzed and their paleoenvironmental interpretation suggests four stages in the Holocene history of the lagoon. Stage A represents a terrestrial environment older than 11 ka and contemporaneous with a low sea level and a distal shoreline. As a consequence of postglacial sea-level rise, a brackish environment, dominated by the species Ammonia tepida and Brizalina britannica, progressively developed in the area between 11–8 ka. It was followed by a normal-salinity environment with Asterigerinata mamilla, B. britannica and Cribroelphidium excavatum as the main species during the period 8–5.5 ka. This Stage B represents a marine advance into the Melides area characteristic of the lower Holocene worldwide. Around 5.5 ka (Stage C), a coastal lagoon environment developed as a consequence of formation of a sandy barrier, which isolated the previous marine setting from the open sea. Assemblages show that the lagoon was dominantly closed with fresh water to very slightly brackish conditions from 5.5->0.5 ka. Only the highly tolerant species Haynesina germanica is found abundantly in the few intervals containing foraminifera dated between >3.4 and <2.5 ka. Finally, Stage D, corresponding to the last >0.5 k.y., reflects human intervention on the lagoon with land reclamation activities and artificial opening of the inlet. Only H. germanica and A. tepida characterize the modern environment. This general pattern is in agreement with microfossil results obtained from other coastal sedimentary sequences studied during recent years in southwestern Portugal and, therefore, is proposed as a possible regional evolutionary model for the last 12,000 years.