Marine environmental legislation is increasingly expressing a need to consider the quality of pelagic habitats. This paper uses the European Union marine strategy framework to explore the concept of good environmental status (GES) of pelagic habitat with the aim to build a wider understanding of the issue. Pelagic ecosystems have static, persistent and ephemeral features, with manageable human activities primarily impacting the persistent features. The paper explores defining the meaning of "good", setting boundaries to assess pelagic habitat and the challenges of considering habitat biodiversity in a moving medium. It concludes that for pelagic habitats to be in GES and able to provide goods and services to humans, three conditions should be met: (i) all species present under current environmental conditions should be able to find the pelagic habitats essential to close their life cycles; (ii) biogeochemical regulation is maintained at normal levels; (iii) critical physical dynamics and movements of biota and water masses at multiple scales are not obstructed. Reference points for acceptable levels of each condition and how these may change over time in line with prevailing oceanographic conditions, should be discussed by knowledge brokers, managers and stakeholders. Managers should think about a habitat hydrography rather than a habitat geography. Setting the bounds of the habitats requires a consideration of dimension, scale and gradients. It is likely that to deal with the challenges caused by a dynamic environment and the relevance of differing spatial and temporal scales, we will need to integrate multidisciplinary empirical data sets with spatial and temporal models to assess and monitor progress towards, or displacement from GES of the pelagic habitat.