The mechanistic simulator of depth filtration of non-Brownian particles in granular beds, which was reported in Burganos et al., 2001, is upgraded and used to investigate the effects of various filter design modes on particle capture efficiency and permeability. The simulation covers all stages of deposition, including extensive pore clogging. The design modes which are examined here are downflow and upflow, in combination with either constant flowrate or constant pressure drop. It is shown that the direction of the macroscopic flow relative to that of gravity has significant effects. Downflow filters clog slower than upflow ones. It is also shown that the modulating functions, which give the effect of the specific deposit on the filtration coefficient and the permeability, depend on whether the flowrate or the pressure drop is kept constant. During the early stages of deposition, the modulating functions are virtually the same for both modes of operation, but in advanced stages of deposition substantial differences are observed. These differences are attributed to the fact that when the flowrate is kept constant (at the expense of a virtually monotonically increasing pressure drop), the flow is channeled through certain connected pathways which are composed of relatively deposit-free pores. Such pores are kept clean because the local interstitial velocity is high. This phenomenon is much weaker or even absent when the pressure drop is kept constant, in which case the flowrate decreases virtually monotonically. Another interesting new result is that both of the modulating functions depend, weakly but noticeably, on depth.