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+.