Introduced and translocated non-native species are a major threat to biodiversity, especially in aquatic habitats. Efforts aimed at the mitigation of impacts and the implementation of preventative measures for the conservation of native biota must rely upon an accurate evaluation of the risks posed by non-native invasive species and are expected to be strengthened by international collaboration. In this study, 76 non-native freshwater fish species of which 48 extant (both introduced and translocated) and 28 horizon were screened for their risk of invasiveness in the neighbouring countries of Croatia and Slovenia under current and future climatic conditions. Using the Aquatic Species Invasiveness Screening Kit (AS-ISK), threshold scores for the Basic Risk Assessment (BRA) and for the combined BRA and Climate Change Assessment (BRA + CCA) allowed to distinguish with a high level of accuracy between low-, medium- and high-risk species – the latter representing ≈70% of the screened species. Brown bullhead Ameiurus nebulosus, round goby Neogobius melanostomus, topmouth gudgeon Pseudorasbora parva and Wels catfish Silurus glanis were the highest-scoring species for Croatia, and Ameiurus nebulosus, snakehead Channa argus and Pseudorasbora parva for Slovenia. There were discrepancies in medium- and high-risk rankings between Croatia and Slovenia for 12 species. Upon comparison of the BRA outcomes with those based on the Freshwater Fish Invasiveness Screening Kit (the predecessor of the AS-ISK), the risk changed for six species in Croatia and five in Slovenia. After accounting for predicted climate change conditions, the BRA + CCA risk scores increased for ≈50% of the species, with western mosquitofish Gambusia affinis, channel catfish Ictalurus punctatus and black carp Mylopharyngodon piceus achieving the highest score increment for Croatia, and round goby Neogobius melanostomus and Chinese (Amur) sleeper Perccottus glenii for Slovenia. The present outcomes will assist decision-makers in the implementation of appropriate measures for the management of extant non-native species and the potential introduction of horizon species. This is important for the regulation of pet trade and aquaculture as well as for management strategies aimed at the conservation of native biodiversity, which in the case of neighbouring countries/jurisdictions will benefit from joint efforts relying on a full risk assessment for the species classified at higher risk of invasiveness.