In the Rhine-Meuse delta many scour holes are present. These scour holes form a potential risk on the surrounding bridges, levees, weirs, dikes and tunnels. In general, scour holes can develop when there is a local change in hydrodynamic conditions or erosive capacity. Extensive research has been done in the past on scour holes close to hydraulic structures in a homogeneous subsoil, however, a large amount of scour holes are not related to hydraulic structures. Additionally, in deltas, the subsoil mostly consists of alternating layers of soil with different erosive capacities. This experimental study focused on a simplified situation of scour holes in heterogeneous subsoil with a three-dimensional character. The bed of the flume consisted of a concrete layer with a hole in the centre in which sand was exposed to the flow. Water depth, flow velocity and the size of the geometry were systematically varied to investigate their influence on scour hole development. Additionally, general observations were performed on the flow structures and scour development in and around the scour hole. It was observed that the scour development is different compared to the results of earlier investigations as a result of the non-erodible top layer. The process of undermining is a limiting factor for sediment transport out of the scour hole. The water depth showed a significantly smaller influence on the scour depth compared to existing empirical formulas. Additionally, the size of the geometry seems to be the most important varied parameter in this study. Relative to the size of the geometry, the scour depth remained approximately equal with different experimental conditions. Compared to two-dimensional experiments, the scour holes became deeper, which suggests importance of three-dimensional flow for scour hole development.