We examine the time-dependent three-dimensional gas-particle flow in an intact wall-flow filter consisting of channels alternatively plugged at each end and a partially damaged filter in which the rear plugs are removed. Our focus is placed on highlighting the differences in the flow pattern and the deposition process between the two geometries. The Navier–Stokes equations are solved for the fluid flow coupled with a Brinkman/Forchheimmer model in order to simulate the flow in the porous walls and plugs. Discrete particle simulation is utilized to determine the nanoparticle trajectories. Using this scheme, we are able to characterize the main features of the flow fields developing in the intact and damaged filters with respect to the Reynolds number and identify those affecting the transport and deposition of particles that have three representative response times. We present fluid velocity iso-contours, which describe the flow regimes inside the channels, as well as in regions upstream and downstream of them. We provide evidence of local recirculating bubbles at the entrance of the channels and after their exit, whereas back-flow occurs in front of the rear plugs of the intact channels. We show that the flow leaves the channels as strong jets that may break up for certain flow parameters, leading to turbulence with features that depend on the presence of the rear plugs. The removal of the rear plugs affects the flow distribution, which, in turn influences the flow rates along the channels and through the walls. We describe the particle trajectories and the topology of deposited particles and show that particles follow closely the streamlines, which may cross the surface of permeable walls for both flow configurations. The distribution of deposited particles resembles the spatial variation of the through-wall flow rate, exhibiting two peak values at both ends of the intact filter channel, and one local maximum near the entrance of the damaged filter channel that is diminished at the exit. We also investigate in detail the particle deposition on the frontal face and indicate that particle accumulation at the edges of the entrance is favored for particles with low response times in flows with high fluid mass rates for both intact and damaged filters. Finally, we examine the filtration efficiency for the defective channels without rear plugs and show that fewer particles are captured as the Reynolds number is increased. A smaller reduction of the filtration efficiency is also predicted with increasing particle size.