SUMMARY A robust, accurate, and computationally efficient interface tracking algorithm is a key component of an embedded computational framework for the solution of fluid–structure interaction problems with complex and deformable geometries. To a large extent, the design of such an algorithm has focused on the case of a closed embedded interface and a Cartesian computational fluid dynamics grid. Here, two robust and efficient interface tracking computational algorithms capable of operating on structured as well as unstructured three‐dimensional computational fluid dynamics grids are presented. The first one is based on a projection approach, whereas the second one is based on a collision approach. The first algorithm is faster. However, it is restricted to closed interfaces and resolved enclosed volumes. The second algorithm is therefore slower. However, it can handle open shell surfaces and underresolved enclosed volumes. Both computational algorithms exploit the bounding box hierarchy technique and its parallel distributed implementation to efficiently store and retrieve the elements of the discretized embedded interface. They are illustrated, and their respective performances are assessed and contrasted, with the solution of three‐dimensional, nonlinear, dynamic fluid–structure interaction problems pertaining to aeroelastic and underwater implosion applications. Copyright © 2012 John Wiley & Sons, Ltd.