Vector ecology is a key factor in understanding the transmission of disease agents, with each species having an optimal range of environmental requirements. Scarce data, however, are available for how interactions of local and broad-scale climate phenomena, such as seasonality and the El Niño Southern Oscillation (ENSO), affect simuliids. We, therefore, conducted an exploratory study to examine distribution patterns of species of Simuliidae along an elevational gradient of the Otún River in the Colombian Andes, encompassing four ecoregions. Larval and pupal simuliids were sampled at 52 sites ranging from 1800 to 4750 m above sea level in dry and wet seasons and during the La Niña phase (2011–2012) and the El Niño phase (2015–2016) of the ENSO; physicochemical measurements were taken during the El Niño phase. Twenty-seven species in two genera (Gigantodax and Simulium) were collected. Species richness and occurrence in each ecoregion were influenced by elevation, seasonality, and primarily the warm El Niño and cool La Niña phases of the ENSO. The degree of change differed among ecoregions and was related to physicochemical factors, mainly with stream discharge. Some putative simuliid vectors of Leucocytozoon, such as G. misitu and S. muiscorum, markedly changed in distribution and occurrence, potentially influencing parasite transmission.