SUMMARY Accurate timing corrections for seismic data recorded by ocean bottom seismometers (OBSs) are essential for a wide range of applications. The synchronization of internal OBS clocks with Global Positioning System (GPS) is typically only possible prior to deployment on the seafloor and upon retrieval. Thus, untracked, clock errors in seismic data may accumulate over the deployment period. The measurement of the clock's offset from GPS at retrieval, referred to as ‘skew’, can be used to correct the data solely under the assumption of a uniform rate of clock drift throughout the whole deployment. However, clock errors can be non-linear. We, therefore, develop a new workflow along with an associated open-source, interactive graphical user interface to estimate clock drift of large aperture OBS arrays. We use the workflow to estimate OBS clock drift curves for 40 OBSs of the large-scale UPFLOW seafloor array in the Madeira–Azores–Canaries region deployed for ∼14 months in 2021–2022. We use the relative shift of daily empirical Green's functions obtained from seismic ambient noise recorded by all available data channels to track clock error. We find that 95 per cent of our OBS clock drift observations have a substantial non-linear component: most maximum deviations to linearity are ∼0.75–1 s (and up to 2 s) occurring mainly halfway through the deployment. We test our drift curves by using them to correct teleseismic earthquake recordings, which enables larger numbers of high-quality P-wave traveltime measurements than when using linear drift corrections. Our drift curves have on average an uncertainty of ∼0.11 s indicating the suitability of the corrected data for future seismological studies such as for seismic tomography, seismicity analysis and moment tensor inversions.