We present a new methodology using bottom pressure recorder (BPR) measurements in conjunction with sea level, water column, and barometric data to assess the long‐term vertical seafloor deformation to a few centimeters accuracy in shallow water environments. The method helps to remove the apparent vertical displacement on the order of tens of centimeters caused by the BPR instrumental drift and by seawater density variations. We have applied the method to the data acquired in 2011 by a BPR deployed at 96 m depth in the marine sector of the Campi Flegrei Caldera, during a seafloor uplift episode of a few centimeters amplitude, lasted for several months. The method detected a vertical uplift of the caldera of 2.5 ± 1.3 cm achieving an unprecedented level of precision in the measurement of the submarine vertical deformation in shallow water. The estimated vertical deformation at the BPR also compares favorably with data acquired by a land‐based GPS station located at the same distance from the maximum of the modeled deformation field. While BPR measurements are commonly performed in deep waters, where the oceanic noise is relatively low, and in areas with rapid, large‐amplitude vertical ground displacement, the proposed method extends the capability of estimating vertical uplifts from BPR time series to shallow waters and to slow deformation processes.