Along the north-Ecuadorian coast, characterized by high cliffs alternating with small plains in correspondence with river mouths, the Ensenada de Atacames, limited backwards by the Cordillera Costanera, consists mainly in a gently sloping surface falling between 3 and 10 m a.s.l., which was the site of an human settlement belonging to the “Atacames culture” (500 B.C.–1500 A.D.). This surface is interrupted seawards by a vertical cliff, subject to a rapid retreat. The pedo-stratigraphic study reveals it was built in a coastal brackish lagoon. The continental shelf facing Atacames is pointed out the presence of a carbonatic bank, remnant of an arrecife of late Pleistocene or early Holocene. As regard to the formation of the lagoon, one has to think to the genesis of a sandy barrier which isolated the waters of the Ensenada from the open sea. Since the Middle Holocene transgression is well known and sands are widely diffused on the carbonatic bank, one can infer that the genesis of the sandy barrier occurs because of their deposition and due to processes of littoral drift. The lagoon was probably formed just after the Holocene Climatic Optimum, by the development of a more and more stable sandy bar, which could have emerged around 3500 BP, during a recognized decrease of the sea level. After the colonization, the Atacames surface could become affected by erosional processes. Taking into consideration the present-day events, the most probable explication of the break of the external sandy barrier, which primed an erosional process, could have been the recurrence of strong ENSO (El Niñ o Southern Oscillation) events.