The National Metrology Institute of Japan (NMIJ) has developed three levels of certified reference materials (CRMs) (NMIJ CRM 7601-a, 7602-a, and 7603-a) for nutrient analysis to provide SI traceability of analysis values of nutrients (nitrate, nitrite, phosphate, and dissolved silica) in oceanographic observations and to enable the comparison of these values across time and space. These property values were determined using the analytical results of multiple analytical methods and standard solutions of inorganic ions and elements as the SI traceability source. Depending on their characteristics, each property value was finally distinguished as a certified value, indicative value, or information. The homogeneity and long-term stability of the CRMs were evaluated on the basis of the International Organization for Standardization (ISO) Guide 35 using the results of continuous flow analysis. The certified values of nitrate and dissolved silica in 7603-a, from the deep Pacific Ocean, could be certified with uncertainties as low as approximately 1%, which is required for the observations. The values for nitrite and phosphate, as well as for relatively low nutrient concentrations, met the minimum requirements for the oceanographic observations, although the uncertainties were slightly higher. In terms of direct distribution from the National Research Institute of Metrology, these CRMs are the first CRMs in the world that can cover a wide nutrient concentration range from that of surface water to that of the deep Pacific Ocean. This development is expected to make the metrological accuracy of nutrient analyses in the observations more robust.