Coastal and tidal environments are valuable ecosystems, which, however, are under pressure in many areas around the world due to globalization and/or climate change. Detailed mapping of these environments is required in order to manage the coastal zone in a sustainable way. However, historically these transition zones between land and water are difficult or even impossible to map and investigate in high spatial resolution due to the challenging environmental conditions. The new generation of airborne topobathymetric light detection and ranging (LiDAR) potentially enables full-coverage and high-resolution mapping of these land-water transition zones. We have carried out topobathymetric LiDAR surveys in the Knudedyb tidal inlet system in the Danish Wadden Sea and the Rødsand lagoon connected to Fehmarnbelt. The overall aims are to: (i) derive characteristic properties of the morphology, surface sediment, the vegetation and the water column in land-water transition zones like rivers, lakes, wetlands, estuaries and coasts; (ii) improve the understanding of the dynamics of these properties in shallow water ecosystems, which are under pressure due to changing environmental conditions driven by climate change; and (iii) develop tools for quantifying geological resources, habitat distributions and system-indicators in land-water transition zones, developed in and for a GIS in order to optimize application by end-users. Here, we present the preliminary results of these two surveys which were carried out at two locations with different environmental settings. We demonstrate the potential of using airborne topobathymetric LiDAR for seamless mapping of land-water transition zones in challenging coastal environments, e.g. in an environment with high water column turbidity and continuously varying water levels due to tides as well as in an environment characterized by a very heterogeneous surface sediment composition.