A three‐part algorithm is described and tested to provide robust bathymetry maps based solely on long time series observations of surface wave motions. The first phase consists of frequency‐dependent characterization of the wave field in which dominant frequencies are estimated by Fourier transform while corresponding wave numbers are derived from spatial gradients in cross‐spectral phase over analysis tiles that can be small, allowing high‐spatial resolution. Coherent spatial structures at each frequency are extracted by frequency‐dependent empirical orthogonal function (EOF). In phase two, depths are found that best fit weighted sets of frequency‐wave number pairs. These are subsequently smoothed in time in phase 3 using a Kalman filter that fills gaps in coverage and objectively averages new estimates of variable quality with prior estimates. Objective confidence intervals are returned. Tests at Duck, NC, using 16 surveys collected over 2 years showed a bias and root‐mean‐square (RMS) error of 0.19 and 0.51 m, respectively but were largest near the offshore limits of analysis (roughly 500 m from the camera) and near the steep shoreline where analysis tiles mix information from waves, swash and static dry sand. Performance was excellent for small waves but degraded somewhat with increasing wave height. Sand bars and their small‐scale alongshore variability were well resolved. A single ground truth survey from a dissipative, low‐sloping beach (Agate Beach, OR) showed similar errors over a region that extended several kilometers from the camera and reached depths of 14 m. Vector wave number estimates can also be incorporated into data assimilation models of nearshore dynamics.