Despite the mounting evidence supporting positive relationships between species abundance and habitat suitability, the capacity of ecological niche models (ENMs) to capture variations in population abundance remains largely unexplored. This study focuses on sympatric populations of hen harrier (Circus cyaneus) and Montagu’s harrier (Circus pygargus), surveyed in 1997 and 2017 in an upland moor area in northwestern Spain. The ENMs performed very well for both species (with area under the ROC curve and true skill statistic values of up to 0.9 and 0.75). The presence of both species was mainly correlated with heathlands, although the normalized difference water index derived from Landsat images was the most important for hen harrier, indicating a greater preference of this species for wet heaths and peat bogs. The findings showed that ENM-derived habitat suitability was significantly correlated with the species abundance, thus reinforcing the use of ENMs as a proxy for species abundance. However, the temporal variation in species abundance was not significantly explained by changes in habitat suitability predicted by the ENMs, indicating the need for caution when using these types of models to infer changes in population abundance.