As neotropical freshwater fish face alarming biodiversity loss, there is an urgent need for more efficient and accurate biomonitoring tools that require less taxonomic expertise than traditional methods. While the analysis of water or sediment environmental DNA (eDNA) has rapidly gained popularity, a growing body of research is investigating ’natural samplers’ - living organisms that aggregate eDNA through their feeding behavior - as tools for biomonitoring. Here, we investigated whether abundant and widely distributed freshwater shrimp could provide a reliable snapshot of local fish assemblages in large neotropical rivers. Multi-marker metabarcoding analysis of shrimp dietary DNA revealed as many species as an intensive 10-day inventory of the study area and nearly three times more species than gillnet-based methods commonly used in surveillance programs. The generalist and opportunistic feeding behaviour of these detritivorous organisms allow for the detection of a broad spectrum of species in terms of size, including small fish overlooked by traditional gillnet-based surveys. Furthermore, most fish taxa were identified at the species level thanks to the availability of nearly exhaustive barcoding reference databases. As the cost and speed of molecular analyses continue to decrease, the relative ease of sampling and processing makes this method particularly suitable for carrying out rapid biodiversity assessments and detecting the localized ecosystem impacts of anthropogenic disturbances, complementing observational approaches that provide data on fish abundance, biomass, or condition.