High‐quality seawater total alkalinity (AT) measurements are essential for reliable ocean carbon and acidification observations. Well‐established manual multipoint potentiometric titration methods already fulfill these requirements. The next step in the improvement of these observations is the increase of the spatial and temporal measuring resolution with minimal personnel and instrumental effort. For this, a rapid, automated underway analyzer meeting the same high requirements as the traditional method is necessary. In this study, we carried out a comprehensive characterization of the flow‐through analyzer CONTROS HydroFIA® TA (Kongsberg Maritime Contros GmbH, Kiel, Germany) for automated seawater AT measurements in the laboratory and in field with overall more than 5000 measurements. Under laboratory conditions, the analyzer featured a precision of ± 1.5 μmol kg−1 and an accuracy of ± 1.0 μmol kg−1, combined in an uncertainty of 1.6 – 2.0 μmol kg−1. High precision (± 1.1 μmol kg−1) and accuracy (−0.3 ± 2.8 μmol kg−1), and low uncertainty (2.0 – 2.5 μmol kg−1) were also achieved during field trials of 4 and 6 weeks duration. Although a linear drift appears to be the typical behavior of the system, this can be corrected for by regular reference measurements giving consistent measurement results. Another advantage of regular reference measurements is the early detection of any kind of malfunction due to its direct impact on the measurement performance. Based on the present study, recommendations for automated long‐term deployments are provided in order to gain optimal performance characteristics, aiming at the requirements for AT measurements.