La Paz Bay (LPB) considered one of the most highly productive bays in the southwestern Gulf of California, Mexico, recently established as Priority Marine Region, supports many species of ecological importance. In this context, daily composites of surface chlorophyll a (Chl-aSAT), sea surface temperature (SST) satellite images derived from the MODIS-Aqua sensor, and a wind intensity index (WI) calculated with data recorded simultaneously at four points along the coast, were used to describe the strong 2015–2016 El Niño impact over the surface chlorophyll pigments in LPB, relative to its average for 2003–2013. Significant relationships between SST, WI (used as environmental factors) and Chl-aSAT (RSST = −0.74, RWI = −0.40, P < 0.01) were found using exponential models for the entire study period, with moderate correlation during El Niño winter condition (December 2015 to March 2016) between SST and Chl-aSAT (RSST = 0.45, P < 0.02). The Chl-aSAT showed unexpectedly low values (∼0.5–1.2 mg m−3) with one month-lag of the winter bloom period jointly with the presence of warmer-than-usual water (∼1.0 °C) and episodes of strong northwesterly winds (speed 8.0–10.0 m s−1) that began in autumn that drove a ∼2 month-lag in its winter peak. The Chl-aSAT and SST winter spatial patterns, showed low Chl-aSAT values (∼−0.5 to −1.0 mg m−3) along the bay and higher-than-usual SST by ∼ 0.5–1.0 °C relative to a year under the La Niña winter condition (2017–2018). This triggered the possible thermocline deepening and the lowest levels of nutrient supply to the photic layer during the El Niño winter episode. Hovmöller diagrams of Chl-aSAT and SST anomalies along the coast revealed a sharp drop to negative anomaly values (∼− 0.7 to −1.2 mg m−3), in-phase but negatively correlated with the SST coastal anomalies (R = − 0.88, P < 0.01). This biophysical coupling played a crucial role in the exceptional drop to the lowest winter Chl-aSAT levels seen in LPB since the MODIS satellite sensor began taking measurements in 2002 (Chl-aSAT values were lower than usual by ∼ 0.9–1.2 mg m −3). Besides the lowest winter levels observed, this research reflected the El Niño signal-driven changes over the basic seasonal average of the LPB climate system The non-significant negative trend observed in the winter average Chl-aSAT values, indicates that LPB may be less resilient to future environmental disturbances.
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