Direct laboratory measurements of in situ water-phase saturation history are used to estimate relative permeability and capillary pressure functions. The magnitude of so-called nonequilibrium effects during spontaneous imbibition is quantified and, if significant, these effects are incorporated within the estimation technique. The primary constraint employed is that curves must increase or decrease monotonically; otherwise, no predetermined functionality is assumed. The technique is demonstrated using water saturation profile histories obtained for diatomite (a low-permeability and high-porosity rock). Results indicate that nonequilibrium effects detected at laboratory scale in low-permeability rocks influence the estimation of unsteady-state relative permeability and capillary pressure.