Analogous to the use of Rayleigh waves in MASW on land, Scholte waves can be used to derive shear wave velocity profiles for the subsurface under water. These profiles are useful for dredging operations, offshore wind farms, oil rigs and pipelines. We have determined the optimal acquisition set up for the detection Scholte waves in shallow water. The nearest offset, receiver spacing and number of channels have been varied in a finite difference model consisting of a water layer on top of a sediment layer and a half space. The best configuration is a nearest offset of 10 m, receiver spacing of 1 m and 48 channels. When the seafloor is not horizontal, the source/receiver spread should follow the topography. When the distance between the source and the sea floor becomes too large, no Scholte waves are detected and subsequently no reliable Vs profile can be retrieved. In order to test the acquisition set up for a more realistic subsurface, a dipping layer and a filled channel structure were modeled. Whereas the inversion results for the dipping layer were satisfactory, the channel structure displayed large differences relative to the model, especially on the flanks.