Ground fissures have occurred in the last four decades across the eastern Thessaly basin (Greece) resulting in damage to the villages of the area. Several studies for the area refer to the over-pumping of ground water as the main reason for their occurrence, causing sediment compaction due to the reduction of the aquifer level. In this paper, we depict the results of a joint geophysical survey trying to determine the subsurface regime of the basin and the exact reasons contributing to the existence of the ground fissures. The focal part of the survey includes gravity measurements for deeper investigation, combined with existing and already presented geoelectrical and electromagnetic data. Several borehole data have also been used for the calibration of the geophysical interpretation. The differential GNSS data of the gravity campaign revealed the ground subsidence of the area, reaching up to 9.16 m. The alpine basement of the area is comprised mainly of metamorphic rocks, such as marbles, mica schists and gneiss-schists, covered by thick fluviοterrestrial and alluvial deposits. Several structural maps were generated in order to delineate the lateral density variations that could be related to fault zones along with the interpretive sections for geological modelling. The alpine bedrock was adumbrated in relatively great depths, with a large anticline of NW-SE direction, rising and separating the basin in two parts. In the east part, the fluvioterrestrial deposits, which are expected to play an important role in the compaction due to their water aquifer, are located only west of this anticline. At the east part, where the old lake Karla was hosted, the alluvial deposits lay directly on the alpine basement in smaller depths. This complicated regime is responsible for differential sediment compaction and the ground subsidence of the surface.