The EU Member States, Norway and the European Commission in 2000 have jointly developed a common implementation strategy (CIS) for implementing Directive 2000/60/EC, the Water Framework Directive (WFD) to ensure consistent implementation. The focus is on developing a common understanding of the technical and scientific implications of the WFD. One of the objectives is the development of non-legally binding and practical Guidance Documents on various technical issues of the Directive. These are targeted at experts who are directly or indirectly implementing the WFD in river basins. The structure, presentation and terminology are therefore adapted to their needs and formal, legalistic language is avoided wherever possible. In 2009 CIS Guidance on Eutrophication Assessment (Guidance Document No. 23) was published, providing guidance for evaluating the impacts of nutrient enrichment, a major cause of failure to achieve good status under the WFD. However, an apparently wide range of nutrient boundary values to support good ecological status had been established by the Member States. Water Directors requested that the CIS Working Group ECOSTAT investigate this issue, and the subsequent work has been led by the UK (Freshwaters), Germany (Saline waters) and JRC. The aim of the work was to establish the reasons for differences between Member States in the development and application of nutrient boundaries, leading to the production of this guidance on best practice. This work is an addition to, and not a replacement for, the earlier guidance on eutrophication assessment. In developing this guidance, a number of tasks have been undertaken. The range of nitrogen and phosphorus boundary values in use by Member States, and the methods used to derive those values has been reported separately, for both fresh and saline waters. Further work was undertaken to investigate nutrient pressure-biological response relationships in the different surface water categories. This work was then used to inform the development of this guide and the associated statistical toolkit. During the project a series of workshops were held involving nutrient experts nominated by Member States. These experts contributed to the development and testing of the guidance and toolkit, and provided details of alternative methods of boundary setting in use in some Member States. The purpose of this report is to provide technical guidance to enable Member States to establish new, or review existing, boundaries for phosphorus and nitrogen to support good ecological status. This should facilitate the establishment of comparable and consistent boundaries across all Member States. However it is recognised that alternative methods of arriving at boundary values may be valid, and use of this guidance and the associated statistical toolkit is ultimately a decision for the Member State. The responses of biological elements to nutrient availability are complex, and vary between water categories. This guidance is not therefore a substitute for the application of ecological knowledge and understanding at a local level. Furthermore, responses to nutrients may be confounded by the impact of other pressures acting on a water body, and our understanding of how to account for multiple stressors is still developing. The guidance does not specifically address how the nutrient boundaries are used to derive an overall classification, or to drive action to control nutrients, both of which may be relevant to the level at which the boundaries are set.