Intertidal mudflats are morphodynamic features present in many estuaries worldwide. Often located between vegetated shores and deep channels they comprise valuable ecosystems and serve to protect the hinterland by attenuating waves. Although mudflats are persistently present on yearly to decadal time scales, little is known on their morphodynamic adaptation to short‐term variations in forcing such as storms, spring‐neap tidal cycles, and sediment supply. This study aims to explore the morphodynamic resilience of mudflats to seasonal variations in forcing. First, we compare transects observed in South Bay, California, at 3‐ to 6‐monthly intervals. Second, we present the results of a process‐based, morphodynamic profile model (Mflat). Mflat is an open source, Matlab code that describes both cross‐shore and alongshore tidal hydrodynamics as well as a stationary wave model. An advection‐diffusion equation solves sediment transport while bed level changes occur by the divergence of the sediment transport field. Mflat reproduces the observed South San Francisco Bay profile in equilibrium with significant skill. Short‐term variations in hydrodynamic forcing and sediment characteristics disturb the profile mainly at the channel‐shoal edge. The modeled profile disturbance is consistent with observations. The modeled profile is remarkably resilient since it recovers to the equilibrium profile within weeks to months. The model results suggest that 3‐monthly observation intervals are probably too long to discriminate processes responsible for the profile disturbance. These processes may include variations in sediment supply, mudflat erodibility, and wave action as well as the spring‐neap tidal cycle.