Local scour below a sagging pipeline is modelled by coupling a fluid flow model with a morphological model of the seabed. The fluid flow model solves spatial-filtered two-dimensional Navier–Stokes equations closed with the standard Smagorinsky subgrid scale model. The morphological change of the seabed due to scouring is calculated through sediment transport model and a continuity equation that governs the conservation of sediment. Using this model, the effects of pipeline sagging on local scour development as well as the characteristics of the flow are investigated. It is found that the increase in the rate of scour ceases when the pipeline is 50–60% diameter below the original seabed level regardless of the sagging speed and time. However, the ultimate scour depth depends on the sagging speed. The ultimate scour depth exceeds one diameter of the pipeline under slow sagging condition and remains almost unchanged with a fast sagging speed. The numerical model is validated against physical model tests and the calculation results agree with experimental results reported in literature.