Geological instability was considered a driver of high biodiversity in Neotropical region, specially for the intense modifications caused by the Andes uplift. However, the effects of landscape dynamics in morphological traits of Amazon freshwater fishes throughout evolutionary time is poorly understand. We integrated the occurrence of freshwater fishes in one or both western (unstable area) and eastern (stable area) sides of Amazon Basin- a major diversity hotspot - with the most recent time-calibrated phylogeny and the newly compiled morphological traits databases of freshwater fishes to track the influence of landscape dynamics in governing evolutionary processes. We evaluated whether geological processes over 20 my ago (presence of Pebas lake) in the Amazon basin affected the morphological diversification of the siluriforms and characiforms (i.e. traits related to swimming). We found that traits related to body shape (i.e. elongation) presented high and significant phylogenetic signal, indicating that evolutionary lineages history is relevant to understand fishes features modification. For siluriforms, we identified higher speed of morphological diversification rate at eastern region, even this region being more geological stable than the western region. However, for characiforms there was no difference found in fish diversification between stable or unstable regions. These pattern must be associated with the high dispersion of lineages from western to eastern after inversion of Amazon riverine course, where lineages found stable conditions for their establishment. Overall, our results highlight the effect of geological instability on evolutionary morphological diversification on Amazon freshwater fish.