Aim: Our goal was to broaden the understanding of the functioning of two Calanus species (C. glacialis and C. finmarchicus). We hypothesized that their ecological traits (size, pigmentation, lipid content, diet, presence of parasites, and stage structure) would vary across four hydrographically distinct fjords. Location: Hornsund, Isfjorden, Kongsfjorden, van Mijenfjorden; Spitsbergen Methods: Morphological, size-based species identification via stereomicroscopy has been supported by molecular methods. Manual image-based measurements of size and lipid sack area have been assisted by machine learning image analyses. Manual image-based color intensity estimations of pigmentation have been supported by HPLC analysis of astaxanthin concentrations. Trophic variability has been assessed through stable isotope composition analyses. Results: The substantial variability in the studied traits of Calanus copepods (represented by CV life stage) highlights their high plasticity and that the traditionally recognized ecological and morphological distinctions between Calanus species are becoming increasingly blurred. This variability was likely influenced by the coexistence of several cohorts from two species, resulting in a mixture of local and advected populations as well as their multiple generations. These observations suggest that under increasing ‘Atlantification’ pressure, we can expect a suite of responses, including size reduction, faster development, mixed reproductive strategies, reduced pigmentation, dietary shifts, diversified lipid accumulation strategies, and the presence of parasites. Main conclusions: Normative C. glacialis individuals (exhibiting typical size and pigmentation traits) were found only in a minority, supporting the necessity for incorporation of genetic methods. Additionally, we introduce a tool for the automatic assessment of crucial traits, such as size and lipid content, using machine learning techniques. Since these traits are largely shared between these congeneric species this automated approach enables more efficient monitoring of their morphological traits across scales relevant for detecting ecosystem shifts in the northern hemisphere, without relying solely on precise and challenging taxonomic identification.