Background <p>Human activities are driving shifts in the distribution of species. This is leading to profound changes in biological communities as some species head towards extinction while there is a spread of pathogenic organisms and non-indigenous species. For efficient and effective management of these shifts it is critical to be able to detect species of interest promptly and accurately. With technological advancements there is an increasing amount of environmental DNA data available to researchers and environmental managers, but it is often not optimally utilized for the detection of species of interest.</p> Results <p>BIOWATCH is a R shiny app which aims to improve the detection of species of interest in metabarcoding datasets. BIOWATCH enables the user to create custom reference databases from a predefined list of species from public databases. Metabarcoding datasets can then be investigated against these custom databases to detect species of interest. Users are also able to visualize the results to assess spatial and temporal patterns of those species.</p> Conclusion <p>BIOWATCH offers a versatile platform that empowers users to interpret metabarcoding results, contributing to improved ecosystem monitoring, conservation planning, and species management in an era of rapid environmental change.</p>