Fish play a crucial role not only for humans but also as vital indicators in assessing the ecological health of aquatic ecosystems, their status, and ecosystem challenges. The recent gathering in Shkodër convened students, diverse specialists from Albania and Montenegro, and cross-border institutions tasked with protecting and managing natural resources in Lake Shkodra, the Buna River, and its delta. The aim was to address regional issues and bolster capabilities in innovative fish monitoring methods within these ecosystems. Beyond issue identification and the imperative for cooperation among stakeholders within and across borders, attendees underwent training in both traditional and innovative fish monitoring techniques, combining theoretical understanding with practical skills. This meeting also marked the initiation of monitoring efforts. Collaborating with RAPA Shkodër, OMP Shkodër, EnvPro, and institutions from Montenegro, data collection will inform subsequent conservation measures aimed at supporting fish populations. Enhanced insights will be derived from DNA analyses, providing a comprehensive overview of fish species within these basins. The significance of this endeavor lies in the Buna River basin’s pivotal role as a vital migratory corridor for fish, bridging marine and freshwater habitats.