A method and apparatus to reduce the noise in three-dimensional phase contrast magnetic resonance velocity measurements exploits the property that blood is incompressible and therefore the velocity field describing its flow must be divergence-free. The divergence-free condition can be incorporated by the projection operation on Hilbert space where the velocity measurements are projected onto the space of divergence-free velocity fields. The reduction of noise is achieved since the projection operation eliminates the noise component that is not divergence-free. Higher quality angiograms are produced due to the noise reduction in the velocity measurement signals.