The Kastrouli Late Bronze settlement in Phocis province, central Greece, has been proved to have been an important center in the periphery of the Mycenaean palaces. It was reused at least partially and was cultivated until the 20th century. The presence of a flat area off the Kastrouli hill and the seasonal flooding nowadays led to the present investigation, questioning the formation of an ancient lake or marsh/swamp. A methodological approach was applied combining the digital elevation model (DEM) and GIS of the wider and confined area, examining slopes between 0 and 5 degrees (0 and 8.75%), with electrical resistivity tomography (ERT) traverses of around 300 and 500 m, reaching a depth of 100 m. The ERT data were rapidly collected on profiles and provided a cross-sectional (2D) plot. It was found that, in the area, there is a basin with a length of 100 m and a depth of around 40–50 m. The sedimentation process over the millennia has filled the basin, with the upper 5–6 m surface layers of the area having a low resistivity. The presence of two natural sinkholes with apparent engineered hydraulic works is noted to conform to drainage and produce a habitable environment, protecting the cultivated land and avoiding a swamp associated with health issues.