Lake sediment characterization, a prerequisite for the vulnerability assessment of lake ecosystems, demands reliable in situ methods for the characterization of the sediment layer composition. A unified characterization of lake sediments within lake ecotopes (open water, open water patches within the reed, and the reed) is still a challenge. Each ecotope is covered by different classical scientific disciplines (hydrography and terrestrial remote sensing to soil physics) with their specific characterization methods. Recently, a complementary tool that bridges the gap between land and hydrographic surveying methods was introduced. It is a non-acoustic device that combines two soil physical sensors (a capacitive sensor and a cone penetrometer) and GNSS-positioning in a measuring system (CSPS). The CSPS enables rapid in situ delineation of water–mud–consolidated lakebed interfaces. The system was successfully applied across ecotopes at the Neusiedler See, a well-mixed shallow lake rich in fine-grained sediments. The geo-referenced vertical CSPS profiles show ecotope-specific layer composition. The effects of wind-induced turbidity, particle size, and electrical conductivity were analysed. The water–mud interface was precisely delineated at the open water due to a persistent high water content gradient, equivalent to a lutocline. The penetration resistance (PR) for open water showed either a shallow and highly compacted consolidated lakebed or a consolidated lakebed with a partially compacted layer above, while in the reed the PR smoothly increased until reaching the deepest penetration depths.