: Environmental DNA (eDNA) is increasingly used in biodiversity monitoring with several collection techniques proposed. Those applied to aquatic eDNA can now be divided into two categories: active and passive sampling. Active sampling involves the deliberate and controlled collection of environmental samples, and the most common method is water filtration. Passive sampling is a more recent technique that involves capturing eDNA by relying on its adsorption to samplers, which can be fabricated from various materials, and submerged for minutes, hours or weeks. In this study, we compared the performance of water filtration and Passive eDNA Sampling (PEDS) with granular active carbon in terms of detected taxa collected from four different sites of the same river system. eDNA samples were amplified for three molecular markers for 18S rRNA, 12S rRNA and COI genes, with primers according to the literature that target invertebrates and vertebrates. The study revealed that PEDS detected on average more species in 18S rRNA and 12S rRNA assays, with 18S rRNA results presenting a significantly higher homogeneity of read variances between samples. Biological communities captured differed between PEDS and filters. The former method retrieved a significant number of microinvertebrates and chironomids (Chironomidae, Diptera), detecting a similar number of vertebrates to filters, but with lower performance in the detection of fish. Notably, both methods performed well with amphibians, successfully identifying all species linked to lotic environments in the studied area. Compared to PEDS, the eDNA capture protocol using filters yielded more sequences identified as ephemeropterans, trichopterans, and acarines. In addition, PEDS was more cost-effective and environmentally sustainable. These findings imply that there is no definitive superior eDNA sampling method. Consequently, in conjunction with studies proposing new methods of eDNA sampling, studies comparing their performance with a broad taxonomic representation will be pivotal
