The Bahia Magdalena-Bahia Almejas (BM-BA) complex is the largest coastal lagoon system in the Mexican Pacific; it is in a transitional zone between temperate and tropical regions. BM-BA has a high biodiversity and is an important source of fishing resources; however, its productivity diminishes during ENSO+ events. This work aimed to compare the impact of the three most intense ENSOs (1982–1983, 1997–1998, and 2015–2016) on their environmental and biological characteristics in the context of global warming. Since 1970, this region has been warming, and the chlorophyll-a is diminishing; however, short-term environmental variations associated with basin-scale processes have modified these trends. The comparison showed that the equatorial influence on the 1997–1998 ENSO was more evident, while the North Pacific conditions and other large-scale environmental processes influenced the other ENSOs: in 1982–1983, the warm signal continued after the ENSO+ ended, and in 2015–2016, it was present before the ENSO+ onset due to the MWH The Blob and probably global warming. High temperatures at the basin scale altered large-scale wind patterns, weakening local upwelling and diminishing the nutrient input. The Equatorial and North Pacific influence on BM varies over time (as expected in a transition zone like BM); however, in recent years, North Pacific warming associated with climate change has probably gained relevance and modulated the effect of ENSO+.