Many subsurface fluid flows, including the storage of CO2 underground or the production of oil, are transient processes incorporating multiple fluid phases. The fluids are not in equilibrium meaning macroscopic properties such as fluid saturation and pressure vary in space and time. However, these flows are traditionally modeled with equilibrium (or steady-state) flow properties, under the assumption that the pore-scale fluid dynamics are equivalent. In this work, we used fast synchrotron X-ray tomography with 1 s time resolution to image the pore-scale fluid dynamics as the macroscopic flow transitioned to steady state. For nitrogen or decane, and brine injected simultaneously into a porous rock, we observed distinct pore-scale fluid dynamics during transient flow. Transient flow was found to be characterized by intermittent fluid occupancy, whereby flow pathways through the pore space were constantly rearranging. The intermittent fluid occupancy was largest and most frequent when a fluid initially invaded the rock. But as the fluids established an equilibrium the dynamics decreased to either static interfaces between the fluids or small-scale intermittent flow pathways, depending on the capillary number and viscosity ratio. If the fluids were perturbed after an equilibrium was established, by changing the flow rate, the transition to a new equilibrium was quicker than the initial transition. Our observations suggest that transient flows require separate modeling parameters. The time scales required to achieve equilibrium suggest that several meters of an invading plume front will have flow properties controlled by transient pore-scale fluid dynamics.