The West Antarctic Peninsula (WAP; figure 1) is one of the most climatically sensitive regions on Earth and one of the most variable. The strong climatic variability gives us the opportunity to study and understand how the ocean responds to—and gives feedback on—climate change, and hence to learn about the key mechanisms that are at work, which might apply around the Southern Ocean as a whole. Data coverage is still inadequate across the Southern Ocean (because of remoteness and harsh conditions) and, despite being better observed than many other regions around Antarctica, the nature of oceanographic and atmospheric change on the WAP is poorly constrained. This theme issue addresses some of the most important and pressing questions surrounding marine system variability at the WAP. How has the WAP changed and how will it change in future? What’s driving these changes? And why is there such an extraordinary degree of spatial and temporal variability in the region? These questions were addressed in two interlinked meetings held in 2017. A 2 day meeting was hosted in May at the British Antarctic Survey (BAS) in Cambridge, UK (co-sponsored by the Southern Ocean Observing System, the Scientific Committee for Antarctic Research and the Scientific Committee for Ocean Research), aimed at gathering and critically assessing a broad view from the international community on the gaps and challenges in WAP oceanographic research. A second meeting was held at the Kavli International Centre at Chicheley Hall, UK (funded by the Royal Society), specifically to identify the key outstanding biogeochemical questions relevant to the WAP, and how they could be addressed through tangible means, including through the integration of physical and biological studies. This theme issue features contributions from attendees of these two associated meetings, focusing on the physical and biological interactions that impact biogeochemical cycling along the WAP, with a view to elucidating the state of the art of the science and elucidating the overarching issues on which future research effort should be prioritized.