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Over much of the world’s surface oceans, nitrate and phosphate concentrations are below the limit of detection (LOD) of conventional techniques of analysis. However, these nutrients play a controlling role in primary productivity and carbon sequestration in these waters. In recent years, techniques have been developed to address this challenge, and methods are now available for the shipboard analysis of nanomolar (nM) nitrate and phosphate concentrations with a high sample throughput. This article provides an overview of the methods for nM nitrate and phosphate analysis in seawater. We outline in detail a system comprising liquid waveguide capillary cells connected to a conventional segmented-flow autoanalyser and using miniaturised spectrophotometers. This approach is suitable for routine field measurements of nitrate and phosphate and achieves LODs of 0.8 nM phosphate and 1.5 nM nitrate.