The scarcity of bathymetric studies in most Turkish lakes does not allow the documentation and the potential causes of lake bottom irregularities. In this study, relatively high-resolution bathymetric data from Lake Sunnet (NW Anatolia) revealed five deep (5.7 to 9.2m) and narrow (10 to 20m) depressions located along the boundary between the lake bottom and the steep lake margins. Analysis of lake level data belonging to dry seasons hints no leakage through these depressions. However, the negative conical shape and weakly developed levees around the holes suggest an upward episodic groundwater discharge for which direct evidence has been absent up to date. A combined hydraulic and soil mechanical model successfully explains the pockmark activity due to the flow of water through conduits in karstic carbonate bedrock. According to sedimentation rates and average depth of pockmarks in Lake Sunnet, and available regional paleoclimate studies, the onset of pockmark activity might coincide with the transition from the Near East Aridification Phase to the humid Beysehir Occupation Phase around 300 BCE in SW and NW Anatolia.