Knowledge on the ecological determinants and evolutionary processes shaping intraspecific variability in the wild remains scarce. It is particularly needed in the context of biological invasions to fully understand the consequences of invasive species on the functioning of recipient ecosystems. Using geometric morphometrics, stable isotopes, and elemental composition analyses, we quantified phenotypic variability (morphological, trophic, and stoichiometric traits) within and among invasive populations of two crayfish species with distinct invasion histories over 23 gravel pit lakes in southwest France. We sampled 12 populations of the red swamp crayfish (Procambarus clarkii Girard, 1852) and 11 populations of the spiny‐cheek crayfish (Faxonius limosus Rafinesque, 1817). We aimed at unravelling the ecological determinants and the mechanisms (neutral or adaptive) underlying the phenotypic variability among invasive populations. We demonstrate that, for each group of traits, P. clarkii and F. limosus display contrasting patterns of variance distribution across three ecological scales (population, sex, individual). Then, we demonstrate that P. clarkii trait variation in body morphology and stoichiometry is associated with both ecological and historical determinants (i.e. predation pressure, intraspecific invasion, and invasion age), and morphological traits in F. limosus vary with ecological factors only (i.e. predation pressure and abundance of P. clarkii). Finally, we highlight that different combinations of neutral and adaptive processes shaped the phenotypic variability in the two species, with a higher contribution of adaptive processes in F. limosus. Overall, these results indicate that F. limosus has already gone through local adaptation in the meta‐population while this has not yet occurred for P. clarkii, which was introduced later. This highlights that these two invasive species might have contrasting effects across ecological scales. Our study emphasises that studying invasive species can provide great knowledge on intraspecific variability and its ecological determinants and evolutionary processes in the wild. Our results also stress the need to focus on intraspecific variability in the context of biological invasions as it can be substantial across wide geographic areas.