We present a two-dimensional computational model of amoeboid cell migration characterised by cell shape changes due to the formation and extension of protrusions known as blebs. Using this model, we numerically study the deformation of the cell membrane during blebbing, as well as the effects of obstacles, such as protein fibres in the extracellular matrix, on the motion of the blebbing cell. The model is established in the framework of Stokes flow. Cell membrane deformation is coupled to membrane tension, membrane bending, membrane–cortex adhesion and cortical activities via the intracellular and extracellular fluid field described by the Stokes equation. By assuming that actin monomers move at constant speed towards the membrane and polymerise when they approach the membrane, our model shows that the cell movement in unconfined space can be sustained. We also study how a migrating cell interacts with obstacles hydrodynamically, allowing us to model cell migration in confined environments and to investigate the effects of confinement on the cell migration speed. Our model can be used to further study how tumour cells move through the extracellular matrix during cancer metastasis.