A time-dependent model of a tidal or wave bottom boundary layer has been developed to quantitatively evaluate the relative influences of vertical advection, turbulent mixing and shear, and near-bed behavior on settlement of planktonic larvae of benthic animals. The settlement behavior of larvae is modeled with a simple flux condition at the bed. This allows full time dependence to be included when determining settlement rates. For tidal oscillations, the model predicts that most settlement will occur at and near periods of slack water, whereas comparatively little settlement will occur during periods of stronger flow. In contrast, there should be little temporal variability in settlement rates associated with short-period wind waves. If larvae exhibit a relatively weak propensity to settle, then the settlement flux is small compared to the advective/turbulent flux of larvae supplied from higher in the water column to regions near the bed. In this case, a description of probability of settlement and a quasi-steady state suspension model fully describe the system. In contrast, when larvae exhibit a high settlement propensity, then the settlement flux is potentially larger than the advective/turbulent flux and the system is controlled by the hydrodynamic supply of larvae to the near-bed region. In this case, net settlement is governed primarily by larval fall velocity (a composite of gravitational sinking plus swimming) and turbulent shear stress. The ecological systems which are controlled by animal behavior or by physical processes may thus be identified by estimates of relatively simple parameters describing these fluxes.