Our ability to numerically predict the interaction between complex topography and three dimensional flow at large scales (∼1 km) has yet to be fully developed. This is the result of our inability to design numerically stable meshes for complex topographies at these spatial resolutions. This paper deals with the numerical simulation of flow over a natural dune field located in the Rio Paraná, NE Argentina. The methodology is based upon the development and application of a new five term porosity algorithm that modifies the mass conservation equation within a regular Cartesian mesh. Bathymetric measurements were made in the field using a multibeam echo sounder which provided an unparalleled topographic dataset to test this new numerical modeling approach. Measurements of flow were made using an acoustic Doppler current profiler and are used as inlet boundary conditions and validation data. The results demonstrate simple flow acceleration due to topographic forcing over the dune stoss and expansion and deceleration over the dune lee.