The idea that “everything is everywhere, but the environment selects” has been seminal in microbial biogeography and marine phytoplankton is one of the prototypical groups used to illustrate this. The argument has typically been that phytoplankton is ubiquitous, but that distinct assemblages form under environmental selection. It is well established that phytoplankton assemblages vary considerably between coastal ecosystems. However, the relative role of compartmentalisation of regional seas and site-specific environmental conditions in shaping assemblage structures, has not been specifically examined. We collected data from coastal embayments falling within two different water compartments within the same regional sea and also characterised by highly localised environmental pressures. We used PCNM and AEM models to partition the effects that spatial structures, environmental conditions and their overlap had on the variation in assemblage composition. Our model explained a high percentage of variation in assemblage composition (59-65%) and showed that spatial structure consistent with marine compartmentalisation played a more important role than local environmental conditions. At least during the study period, surface currents connecting sites within the two compartments failed to generate sufficient dispersal to offset the impact of differences due to compartmentalisation. In other words, our findings suggest that, even for a prototypical cosmopolitan group, everything is not everywhere.