This paper shows an overview of extensive geotechnical and geological investigation of soils around cover collapse sinkholes that appear in a constrained area around the Mečenčani and Borojevići villages following the 2020–2021 Petrinja earthquake sequence. A total of 122 new and 49 pre-existing historical sinkholes were recorded, mapped, and classified during the geotechnical reconnaissance fieldwork. Many sinkholes collapsed over a small area, a relatively rare phenomenon associated with earthquakes, thus motivating soil investigations to understand associated failure mechanisms and underlying conditions better. This paper shows an overview of triaxial test data in synergy with soil water retention curves of unsaturated soils detected in the area, along with standard physical soil testing data. The soil in the area consists of a 4–10 m thick clayey cover with sporadic gravel lenses. Clays are mostly over-consolidated, with varying degrees of saturation ranging from very small to fully saturated. Underneath are intensely karstified Miocene carbonate rocks. Seasonal and climate-change-induced variations in the groundwater table interact with the artesian/subartesian karst aquifer, thus affecting the suction and the shear strength. In addition, soil water retention curves indicate that desaturation is possible for deeper groundwater table levels and can further affect effective stress, shear strength, and interparticle tensile forces. Collapsed sinkholes have predominately vertical walls, indicating brittle failure of a cohesive cover with varying degrees of saturation. Based on the specific geomechanical properties of soils, this paper offers several hypotheses of failure mechanisms because of the synergy of earthquake-induced dynamic loading and hydro-mechanical interactions of unsaturated soil layers and pore pressure dynamics between two interconnected aquifers.