Accurate and precise marine CO2 system measurements are important for marine carbon cycle research and investigations of ocean acidification. Seawater pH is important because it can be used to characterize a wide range of chemical and biogeochemical processes. Saturation states of calcium carbonate minerals, which are directly proportional to carbonate ion concentration ([CO32−]), influence biogenic calcification and rates of carbonate dissolution. Spectrophotometric pH and carbonate ion measurements can both benefit greatly from the high sensitivity, stability, consistency and processing speed made possible through automation. Spectrophotometric methods are well-suited for shipboard, underway and in situ deployments under harsh conditions. Spectrophotometric pH measurements typically have a reproducibility of 0.0004–0.001 for shipboard and laboratory measurements and 0.0014–0.004 for in situ measurements. Shipboard spectrophotometric measurements of [CO32−] are becoming common on research expeditions. This review highlights the development of methods and instrumentation for spectrophotometric pH and [CO32−] measurements, and discusses the pros and cons of current technology. A comprehensive summary of the analytical merits of different flow analysis instruments is given. Aspects of measurement protocols that bear on the quality of pH and [CO32−] measurements, such as indicator purification, sample pretreatment, etc., are also described. Based on three decades of experience with seawater analysis, this review includes method recommendations and perspectives directly applicable or potentially applicable to pH and [CO32−] analysis of seawater.