This dataset documents the abundance (cells L⁻¹) and taxonomic composition of microplankton in the Reloncaví Sound during the austral spring 2023–summer 2024 transition. Discrete water samples were collected at four stations along the estuarine gradient at the surface and at the fluorescence maximum depth. Diatoms, dinoflagellates, ciliates, nanoplankton, and silicoflagellates were preserved and enumerated by light microscopy following the Utermöhl (1958) sedimentation method.