In ferromagnet/superconductor bilayer systems, dipolar fields from the ferromagnet can create asymmetric energy barriers for the formation and dynamics of vortices through flux pinning. Conversely, the flux emanating from vortices can pin the domain walls of the ferromagnet, thereby creating asymmetric critical currents. Here, we report the observation of a superconducting diode effect (SDE) in a NbSe2/CrGeTe3 van der Waals heterostructure in which the magnetic domains of CrGeTe3 control the Abrikosov vortex dynamics in NbSe2. In addition to extrinsic vortex pinning mechanisms at the edges of NbSe2, flux-pinning-induced bulk pinning of vortices can alter the critical current. This asymmetry can thus be explained by considering the combined effect of this bulk pinning mechanism along with the vortex tilting induced by the Lorentz force from the transport current in the NbSe2/CrGeTe3 heterostructure. We also provide evidence of critical current modulation by flux pinning depending on the history of the field setting procedure. Our results suggest a method of controlling the efficiency of the SDE in magnetically coupled van der Waals superconductors, where dipolar fields generated by the magnetic layer can be used to modulate the dynamics of the superconducting vortices in the superconductors.