Phytoplankton community composition is important in establishing ecosystem structure and function. Intuitively, we recognize that water movements must be important for modifying spatial gradients and plankton diversity. However, identifying boundaries and exchange between habitats in the open ocean is not straightforward. Here, we use the abundance of nine phytoplankton species closely sampled in a mesoscale frontal system in the northeastern North Sea as a proxy for community composition and explore the relationship between phytoplankton biogeography and transport patterns. Subsurface community distributions could be related to modeled patterns in water movement. A methodology for analyzing pelagic diversity that includes a representation of plankton community composition and an Eulerian connectivity tracer was developed, and the relative importance of connectivity and geographical distance for phytoplankton species composition analyzed. The connectivity tracer identifies timescales and dispersal barriers in the open ocean. Connectivity was found to be superior in explaining pelagic plankton diversity and found to be a prerequisite for understanding the pelagic phytoplankton composition. This approach is a valuable tool for establishing the link between ocean transports, ecosystem structure and biodiversity and for informing the placement of marine protected areas.