For many water management issues of shallow lakes with non-consolidated sediments hydrographic surveys of the open water area and reed belt areas are required. In the frame of water management strategy for the steppe lake Neusiedler See, located between Austria and Hungary, a hydrographic survey was conducted. In the open water area (water depth ≥1 m) a sediment echosounder was used. To validate these measurements and to distinguish between water, mud, and sediment layers in the shallow lake and reed belt area additional measurements were needed. As no common standard methods are available yet, we developed a measurement system based on two commonly applied soil physical measurement techniques providing reproducible physical values: a capacitive sensor and a cone penetrometer combined with GNSS-positioning enable dynamic measurements of georeferenced vertical water-mud-bedsediments profiles. The system bases on site-specific calibrated sensors and allows instantaneous, in situ measurements. The measurements manifest a sharp water-mud interface by a sudden decline to smaller water content which is a function of the dielectric permittivity. A second decline indicates the transition to compacted mud. That is concurrently the density where the penetrometer starts registering significant penetration resistance. The penetrometer detects shallow lakebed-sediment layers. Within the lake survey this measurement system was successfully tested.