The uncertainty of estimating relative channel impulse responses (CIRs) obtained using the radiated signature from a ship of opportunity is investigated. The ship observations were taken during a 1.4 km (11 min) transect in a shallow water environment during the Noise Correlation 2009 (NC09) experiment. Beamforming on the angle associated with the direct ray-path yields an estimate of the ship signature, subsequently used in a matched filter. Relative CIRs are estimated every 2.5 s independently at three vertical line arrays (VLAs). The relative arrival-time uncertainty is inversely proportional to source bandwidth and CIR signal-to-noise ratio, and reached a minimum standard deviation of 5 μs (equivalent to approximately 1 cm spatial displacement). Time-series of direct-path relative arrival-times are constructed for each VLA element across the 11 min observation interval. The overall structure of these time-series compares favorably with that predicted from an array element localization model. The short-term standard deviations calculated on the direct-path (7 μs) and bottom-reflected-path (17 μs) time-series are in agreement with the predicted arrival-time accuracies. The implications of these observed arrival-time accuracies in the context of estimating sound speed perturbations and bottom-depth are discussed.