Freshwater biodiversity is rapidly declining worldwide, especially in tropical island environments which appear to be particularly vulnerable to alien species. Monitoring biodiversity using effective methods is crucial for conservation efforts. This study aims to examine the capacity of the eDNA-based method to provide accurate measures of fish and crustacean biodiversity, and how it can be implemented in the French West Indies. To this end, we conducted eDNA and electric fishing capture-based surveys in parallel, both upstream and downstream, in nine Guadeloupean rivers and during two different seasons. While both methods were congruent in terms of species richness and composition, the eDNA-based method generally exhibited greater efficacy and reliability in assessing biodiversity. The exception to this trend was observed during the second campaign for the crustacean community. The quantitative data (the numbers of individuals and percentages of sequences) also proved to be uncorrelated for crustaceans during the second campaign, indicating that further knowledge of crustacean biology is needed. Nevertheless, the eDNA-based method was able to detect the presence of alien, rare and cryptic species, showing that it can be used in tropical island conditions for biodiversity assessment or conservation purposes.