This study assessed the impact of ENSO events in the seasonal and interannual variability of the sea surface temperature (SST) and phytoplankton biomass (expressed as chlorophyll-a, Chl-a levels) obtained from Moderate Resolution Imaging Spectroradiometer (MODIS) satellite products from June 2002 to December 2018, in two contrasting regions of the southern Gulf of California, the connection between the gulf and the Pacific Ocean, and the coastal region off Mazatlán. The generated dataset was compared with the El Niño–Southern Oscillation (ENSO) indices and a local wind-derived coastal upwelling index (CUI) computed in the coastal region off Mazatlán from the ERA5 monthly average wind. In this region, the results showed that the prevailing northwesterly winds reached 4 m s−1; however, southwesterly winds were observed during summer, mainly from June to August. The CUI showed values of up to 35 m3 s−1 per 100 m of coastline. The prevailing winds induce upwelling most of the year, with peaks in winter more intense during La Niña than during the El Niño event. Regarding SST and Chl-a levels, changes were observed with clear seasonal, semiannual, annual, and interannual variability, with 2.8 and 3.7 years of periodicities. In the coastal zone, seasonal values were maximum SST values (30–31 °C) during the summer and minimum values (20–22 °C) during the winter. The Chl-a levels showed an inverse trend, with minimum values (0.1–1.00 mg m−3) during summer and maximum values (>2 mg m−3) during winter. In the P1 site, in the connection between the gulf and the Pacific Ocean, the results showed during summer maximum SST values (29.5–31 °C) and minimum Chl-a (<0.2 mg m−3), while during winter minimum SST values (21–23 °C) and maximum Chl-a (0.3–2.0 mg m−3). Changes were also observed in both parameters owing to El Niño (high SST, low Chl-a levels) and La Niña (low SST, high Chl-a levels) conditions, which were confirmed by spectral and wavelet analyses. During the study period, La Niña conditions occurred during 2005/2006, 2007/2008, a multiyear event in 2010/2012, and 2017/2018, while El Niño conditions occurred during 2002/2003, 2006/2007, 2009/2010, and a multiyear event 2014/2016. Regarding their frequency, La Niña event occurred twice with a frequency corresponding to two years, and El Niño had a recurrence interval of between three and four years.