The microzooplankton community structure (species abundance, biomass, diversity) was investigated at a coastal marine station on the South-West Atlantic Ocean (34°23′S–53°45′W, Uruguay). This is a hydrographically complex site within the Subtropical Convergence zone of the SW Atlantic where knowledge of the microzooplankton is particularly scant. The main goal was to perform a first characterization of that community and evaluate its association to environmental drivers along an annual cycle. Oceanographic variables (temperature, salinity, irradiance, nutrients, chlorophyll-a) and ciliates (aloricate and loricate), and dinoflagellates were recorded monthly from July 2019 to June 2020. Over 100 microzooplankton taxa belonging to approximately 30 families and 40 genera were identified, including several subtropical and subantarctic species. Community structure followed wide transitions at the seasonal scale – particularly between summer and winter as subtropical taxa alternated with euryhaline taxa from colder subantarctic waters. The core environmental variables (temperature, salinity and dissolved inorganic nitrogen [DIN]) explained overall variance in microzooplankton community assembly. During summer, high temperatures (20.3, 16.3–22.4°C) and low nutrients (DIN: 3.5, 0.7–6.7 μM; PO4: 1.0, 0.8–1.5 μM) benefited the development of aloricate ciliates. A nutrient pulse in winter posed favourable stoichiometric conditions and the numerical abundance was dominated by dinoflagellates and loricate ciliates in the following months, while diversity remained highest (taxonomic richness: 36 [22–46]; Shannon–Wiener index: 2.5 [1.9–2.8]). Results suggested that the microzooplankton community at the study site is mainly structured by hydrographic variability linked to the seasonal replacement of offshore water masses that differed in thermohaline properties and nutrient levels, and local processes.