The Global Ocean Ship-based Hydrographic Investigations Program (GO-SHIP) brings together scientists with interests in physical oceanography, the carbon cycle, marine biogeochemistry and ecosystems, and other users and collectors of ocean interior data to develop a sustained global network of hydrographic sections as part of the Global Ocean Climate Observing System. A series of manuals and guidelines are being produced by GO-SHIP which update those developed by the World Ocean Circulation Experiment (WOCE) in the early 1990s. Analysis of the data collected in WOCE suggests that improvements are needed in the collection of nutrient data if they are to be used for determining change within the ocean interior. Production of this manual is timely as it coincides with the development of reference materials for nutrients in seawater (RMNS). These RMNS solutions will be produced in sufficient quantities and be of sufficient quality that they will provide a basis for improving the consistency of nutrient measurements both within and between cruises. This manual is a guide to suggested best practice in performing nutrient measurements at sea. It provides a detailed set of advice on laboratory practice for all the procedures surrounding the use of gas-segmented continuous flow analysers (CFA) for the determination of dissolved nutrients (usually ammonium, nitrate, nitrite, phosphate and silicate) at sea. It does not proscribe the use of a particular instrument or related chemical method as these are well described in other publications. The manual provides a brief introduction to the CFA method, the collection and storage of samples, considerations in the preparation of reagents and the calibrations of the system. It discusses how RMNS solutions can be used to “track” the performance of a system during a cruise and between cruises. It provides a format for the meta-data that need to be reported along side the sample data at the end of a cruise so that the quality of the reported data can be evaluated and set in context relative to other data sets. Most importantly the central manual is accompanied by a set of nutrient standard operating procedures (NSOPs) that provide detailed information on key procedures that are necessary if best quality data are to be achieved consistently. These cover sample collection and storage, an example NSOP for the use of a CFA system at sea, high precision preparation of calibration solutions, assessment of the true calibration blank, checking the linearity of a calibration and the use of internal and externally prepared reference solutions for controlling the precision of data during a cruise and between cruises. An example meta-data report and advice on the assembly of the quality control and statistical data that should form part of the meta-data report are also given.