A new method is presented for identifying potential pipeline problems, such as hazardous exposures. This method comprises a newly developed sand wave amplitude and migration model, and an existing pipeline–seabed interaction model. The sand wave migration model is based on physical principles and tuned with field data through data assimilation techniques. Due to its physical basis, this method is trusted to be more reliable than other, mostly engineering-based methods. The model describes and predicts the dynamics of sand waves and provides the necessary bed level input for the pipeline–seabed interaction model. The method was tested by performing a hindcast on the basis of survey data for a specific submarine gas pipeline, diameter 0.4 m, on the Dutch continental shelf. Good agreement was found with the observed seabed–pipeline levels. The applicability of the method was investigated further through a number of test cases. The self-lowering of the pipeline, in response to exposures due to sand wave migration, can be predicted, both effectively and efficiently. This allows the use of the method as a tool for pipeline operation, maintenance and abandonment.