In the Philippines, trade in non-native aquatic organisms for ornamental purposes and food consumption has been responsible for their large-scale importation since the 1940s. These non-native organisms, and especially invasive fishes, represent one of the major threats to global biodiversity. However, little is known of the potential threats they pose to native species and ecosystems in the Philippines, where a sound risk analysis strategy is needed to control and manage non-native species. As a case study, nonnative freshwater fish species, both extant and horizon, were screened with the Aquatic Species Invasiveness Screening Kit (AS-ISK) for their risk of being or becoming invasive in Lake Taal – a volcanic crater lake of conservation value. Of the 45 species (13 extant and 32 horizon), 68.9% and 91.1% were ranked as high or very high risk, respectively under current and future climate conditions. This study, which provided evidence that led the Philippines government to adopt the AS-ISK decision-support tool for identifying potentially invasive aquatic species in other water bodies of the country, highlights the need for a comprehensive management strategy to avoid future non-native species introductions and mitigate adverse impacts from extant non-native species.