The GEOTRACES program requires the analysis of large numbers of seawater samples for ^(232)Th, ^(230)Th, and ^(231)Pa. During the GEOTRACES international intercalibration exercise, we encountered unexpected difficulties with recovery and contamination of these isotopes, ^(232)Th in particular. Experiments were carried out to identify the source of these issues, leading to a more streamlined and efficient procedure. The two particular problems that we identified and corrected were (1) frits in columns supplied by Bio-Rad Laboratories caused loss of Th during column chemistry and (2) new batches of AG1-X8 resin supplied by Bio-Rad Laboratories released more than 100 pg of ^(232)Th during elution of sample. To improve yields and blanks, we implemented a series of changes including switching to Eichrom anion exchange resin (100-200 μm mesh) and Environmental Express columns. All Th and Pa samples were analyzed on a Neptune multi-collector inductively-coupled-plasma mass spectrometer (MC-ICP-MS) using peak hopping of ^(230)Th and ^(229)Th on the central SEM, with either ^(232)Th, ^(236)U (or both) used to monitor for beam intensity. We used in-house laboratory standards to check for machine reproducibility, and the GEOTRACES intercalibration standard to check for accuracy. Over a 1-y period, the 2 s.d. reproducibility on the GEOTRACES SW STD 2010-1 was 2.5% for ^(230)Th, 1.8% for ^(232)Th, and 4% for ^(231)Pa. The lessons learned during this intercalibration process will be of value to those analyzing U-Th-Pa and rare earth elements as part of the GEOTRACES program as well as those using U-series elements in other applications that require high yields and low blanks, such as geochronology