ABSTRACT This study aimed to characterize their Spatio-temporal distribution of hydrological variables and plankton during neap tides in Bahía Magdalena, a subtropical lagoon south of the California Current. We compare data from surface and bottom waters of stations located inside the lagoon with those near the bay's mouth and between surface and bottom. The availability of nutrients and the chlorophyll-a are associated primarily with the intense upwelling activity in spring. Due to direct marine influence, this relationship was more significant at the inlet than inside the lagoon, especially at the bottom. During the intense upwellings marine influence is maintained even during neap tides. The wind probably causes the homogeneous distribution in most variables within the bay's surface; this may also contribute to the re-suspension of nutrients due to vertical water column mixing. Abiotic variables were not linearly related with zooplankton biovolume and the density of diatoms and dinoflagellates. Phytoplankton was composed mainly by the micro fraction and diatoms during spring and nanoplankton in the warmest season of the year; however, the strong upwellings at the spring's end caused a HAB composed for diatoms. Chlorophyll-a concentration and diatoms were more abundant inside the lagoon and could explain the lower nutrient concentration of that zone. Zooplankton biovolume seasonality differed from other years, with higher values during winter and a significant decreasing trend throughout the year, resulting from the phytoplankton variability. Upwelling and wind variability explains the high biological productivity observed over most of the year.