Despite the importance of fog as a supplementary moisture source in many dryland ecosystems, little is known about the effects of global climate change and natural climate variability on fog regimes. Here, we examined the long‐term (1966-2022) fog trend and the underlying drivers in the typical fog‐dominated Namib Desert. A 9‐year event‐based fog isotope data set (2014-2022) from the Namib Desert was used to classify three different fog types with isotopically distinct moisture origins. We further examined the daily amount of three types of fog in El Niño and non‐El Niño years and their influencing mechanisms. The results showed an overall reduction in fog water availability after 1996. A positive correlation was observed between the simple moving average (SMA) of the annual mean air temperature and the SMA of the annual fog amount from 1970 to 1996, followed by a negative correlation from 1996 to 2022. The 9‐year event‐based fog amount data set revealed an increase in fog formation in El Niño years. Furthermore, the unique fog isotope data set showed that the daily amounts of both ocean‐ and locally generated fog were intensified during the El Niño years over the past decade. We attributed the intensification of advection fog to more frequent and stronger northwesterly winds in El Niño years. Plant transpiration could provide a critical water source for intensifying locally generated fog in El Niño years. Our findings offer critical insights into the acclimation of organisms in fog‐dependent and water‐limited ecosystems under a warming climate.