Micro-estuaries and micro-outlets represent small coastal waterbodies that differ in their relative salinity and size, with the former being larger, more saline (mesohaline versus oligohaline), and exchanging with the sea more often than the latter. There are thousands of these waterbodies along the world’s coastline, yet few of these very small systems have been identified and studied. We investigated systematic differences between micro-estuaries and micro-outlets in terms of phytoplankton community composition, including spatio-temporal variation in both community structure and biomass (chlorophyll-a). A multivariate analysis was used to assess differences in environmental variables, biomass and phytoplankton community composition across four seasons and the two waterbody types. A total of 260 (63 families) and 244 (74 families) phytoplankton taxa were identified within the micro-estuaries and micro-outlets, respectively. Nano- and picoplankton were the dominant groups in micro-estuaries, and pico- and microplankton in micro-outlets. Micro-estuaries were rich in phytoplankton taxa representative of marine, estuarine and freshwater conditions, with a successional sequence in dominance evident, from Chlorophyta during winter to Bacillariophyta in spring and Cyanophyta in summer. By contrast, micro-outlets were mostly dominated by freshwater taxa, with Chlorophyta remaining the dominant group across all four seasons. Higher phytoplankton biomass was recorded during the winter when increased nutrients were available following catchment flooding. Seasonal switching in phytoplankton was reflected not only in changing dominance patterns in both habitat types but also in complete replacement of some species in micro-outlets, despite Chlorophyta remaining dominant. Such temporal turnover, which is often accompanied by predictable seasonal changes in environmental conditions, can promote overall species richness by allowing more taxa to coexist in a single environment through temporal niche segregation.