This paper presents the results of a geoarchaeological study undertaken in Upper Egypt, in the western part of the Karnak Temples complex. The geoarchaeological approach helps to better understand the fluvial dynamics of the Nile in the proximity of the Pharaonic site during the late Holocene. Until recently, most researchers assumed that Karnak was built on a fluvial island and that a large basin connected to the Nile was built in front of the first pylon during the dynastic period. However, recent excavations conducted by the archaeologists of the Supreme Council of Egyptian Antiquities revealed a jetty or quay with probable direct access to the Nile. Therefore in order to reveal in more detail the landscape and waterscape changes in the most western part of Ancient Karnak, a palaeoenvironmental study was conducted. We studied several stratigraphic profiles, manual boreholes (maximum depth of 5.50 m) and percussion drillings (maximum depth of 25 m). Sedimentological and magnetic susceptibility analyses helped to characterize Nile River deposits and to identify the presence of aeolian deposits (associated with wadi fan deposits) in the lower part of the drillings. Fluvial dynamics characterized by flood events, sandy accretions and thick Nile silts/clay deposits are presented and discussed here for later palaeoenvironmental reconstruction. Accurate leveling of the different profiles and boreholes, together with a topographic survey, allow us to recover long sedimentological sequences and to correlate the different sedimentary units. Finally, in order to obtain a chronostratigraphic sequence, radiocarbon dates were obtained from wood, charcoal and ash samples (analyses undertaken at the laboratory of radiocarbon dating of Ifao, Cairo, Egypt). The presence of the Nile River in front of the first pylon in Karnak is attested from the end of the Second Intermediate Period (SIP, ca 1600 BC) until the end of Roman Times (ca. 350 AD), which both correspond to two main phases of Nile River floods.