From a detailed geological study of the ER-1 borehole drilled in the Urdaibai upper estuary, a typical filling-up sedimentary sequence where fluvial gravels are stratigraphicaly covered by brackish intertidal materials has been observed. On top of these, a tidal salt-marsh environment is located. A progressive subaerial exposition and the development of pedogenetic processes (edaphic horizons or palaeosoils) were accelerated by very recent anthropogenic actions as cultivation and surface materials supply. It has been recorded the sedimentary filling and lateral migration of different estuarine environments in this area during the Holocene. Related to possible historical harbour activities in the studied zone, no modifications of the sedimentary dynamics and evolution suggesting a significative ancient human activity (dredgings, excavations, dumpings, …) have been identified.