Global warming is significantly impacting coastal ecosystems, modifying the composition and abundance of microphytoplankton species assemblages. This study investigated the effects of prolonged anomalously warm conditions, particularly during El Niño events, on environmental conditions and net primary productivity (NPP) in Alfonso Basin, Southwest Gulf of California. We combined an in situ monthly time series of biogeochemical variables collected from 2022 to 2023 with 2003–2023 monthly satellite-derived data to identify the well-known seasonal pattern with a higher dinoflagellates/diatoms proportion in the summer and autumn and a lower dinoflagellate/diatom proportion in winter and spring. However, it remains unclear how this ratio has shifted under prolonged interannual anomalously warm conditions. Satellite 2003–2023 sea surface temperatures (SST) increased in an inverse relationship with mixed layer depth (MLD) and NPP, particularly from 2014 to 2023, when predominated SST positive anomalies. These changes were associated with decreased northwesterly winds, enhanced water column stratification, and the early influx of tropical seawater mass, all of which were driven by the transition from La Niña to El Niño event that occurred between June and December 2023. This interannual “tropicalization” phenomenon overall decreased microphytoplankton abundance and a shift in community composition increasing dinoflagellate/diatom ratio. We concluded that the interannual and decadal climate variability strongly modulate the dinoflagellate/diatom ratio dynamics. Anomalous warming events, such as those associated with El Niño and marine heat waves drive multi-year hydrological changes in the subtropical Alfonso Basin, resulting in an elevated dinoflagellate/diatom ratio under conditions of anomalous warm temperatures, increased stratification, and prevailing oligotrophic epipelagic conditions.
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