The Bay of La Paz (BLPZ), located in the southwestern Gulf of California, is a region of significant biological productivity and strong environmental variability that remains to be understood. In particular, the spatial signature of different El Niño-Southern Oscillation (ENSO) conditions and their impact on the ecology of the bay remains puzzling because of contrasting field observations. In this context, the available satellite-derived data on surface chlorophyll (ChlSAT), sea surface temperature (SST) derived from the MODIS-Aqua sensor, together with surface wind intensity (WI) derived from reanalysis datasets from the period 2003–2018 were analyzed to identify the influence of local and remote forcing over the interannual variability of chlorophyll pigment concentration in BLPZ using WI, SST, and the Oceanic El Niño Index (ONI) as environmental factors. Significant relationships between environmental factors and ChlSAT were found using exponential models, with the higher slopes and correlations during La Niña events. Empirical orthogonal function (EOF) analysis was used to extract the principal mode of the ChlSAT and SST interannual variability. The first mode (EOF1) accounted for 64% and 89% of the ChlSAT and the SST interannual variance, respectively, showing a strong gradient along the coast of the bay. The corresponding amplitude of the ChlSAT mode was significantly correlated with the independent variables PC1SST, ONI, and WI anomalies (RSST = − 0.60, RONI = − 0.57, and RWI = 0.44, P < 0.001). Monthly time series of ChlSAT anomalies along the coast where examined as a function of each independent variable using a multiple linear regression analysis (LRA), which revealed that during the 2005 to 2013 period, high peaks of positive ChlSAT anomalies in the central and southern coast were related to cold ENSO events and favorable wind forcing, which smoothed the effect of weak and moderate El Niño episodes. This period of high biological productivity was only interrupted by the strong and long 2015–2016 El Niño event. Since late 2013, the ChlSAT and the WI anomalies showed a sharp drop to negative anomaly values, which may be the result of complex interactions of physical and biological processes observed during strong warm ENSO events, showing one peak of persistent warm SST anomalies via a weakening of the wind intensity (i.e., from atmospheric teleconnection) and a second one due to the oceanic connection. It is confirmed that BLPZ maintains high pigment concentration levels, comparable to those reported on the mainland coast of GC, where only strong warm ENSO episodes cause changes in chlorophyll concentration.
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