The Northern Patagonian shelf (35–42°S SW South Atlantic) is a transitional area between the subtropical and subantarctic domains, where the shelf shifts from source to sink of atmospheric CO2. In the southeast portion (39–42°S, 61–55°W) of this area, winds interact with different water masses and picture a complex circulation that supports two productive frontal systems: the Mid‐Shelf Front (MSF) and the Patagonian Shelf‐break Front. We combined remote sensing (e.g., monthly surface chlorophyll a over the period: September–December 2002–2021), reanalysis (winds and surface currents), and in situ measurements from three cross‐shelf cruises in spring 2016, 2017, and 2019, to assess the underlying drivers of phytoplankton distribution. The anomalous high chlorophyll concentration in the MSF in spring 2016 was related to enhanced water mass retention by N‐NE winds. Contrasting phytoplankton assemblages emerged related to stratified waters in the shelf influenced by the Patagonian Current and vertically mixed waters at the continental edge (Malvinas Current). Large diatoms prevailed in the outer shelf followed by dinoflagellates, while nanoflagellates and microzooplankton dominated in the mid‐shelf. Furthermore, thickness of the subsurface chlorophyll maximum was broader in the early spring than in a more advanced state of the bloom where the coccolithophore Emiliania huxleyi was abundant. We showed that different time‐scale physical processes—winds, surface currents and vertical mixing—are underpinning the development of spring blooms with different taxa composition in the Patagonian shelf, where different water masses define the hydrological complexity that led to patchy phytoplankton.