Investigations into the distribution and ecology of stream species are often hindered by the challenges of working in these systems. Stream species are difficult to inventory due to the complexity of topography and vegetation in streambeds and riparian areas, water turbidity and flow rate, low densities of individuals, cryptic coloration, and the use of microhabitats. Due to these and other factors, surveys for native and exotic species in streams can be expensive and inaccurate. For example, a major challenge in amphibian decline research is that amphibians can be difficult to detect, especially in streams. Electrofishing techniques have high success for detection of aquatic vertebrates in many cases, but can be time consuming and difficult to apply in streams, and may cause injury to peptides sh2 Target and non-target species. Researchers have been using DNA from feces, urine, hair, feathers, shed skin, and eggshells to detect terrestrial vertebrate species for the past decade, and detection of microbial species using environmental DNA found in soil and seawater is revolutionizing species inventories and enabling efficient disease detection. Recently, the reliable detection of aquatic vertebrate species using eDNA in water was confirmed in wetlands and in a large river and canal system. Using eDNA to detect rare and secretive species in streams could increase accuracy and decrease costs of surveys, increase the number of sites sampled per unit effort, refine distribution and extinction records, and provide early detection of invasive species in these systems, without any risk to the species. However, the fast flow of streams may move shed cells away from their source at a rate prohibitive to eDNA collection. To evaluate the potential for using eDNA to survey for stream species, we collected water samples from five small headwater streams in two seasons and tested them for DNA of two amphibian species known to be present at the sites. To achieve this, we designed species-specific primers and tested multiple DNA extraction and PCR protocols designed to amplify low quality DNA templates. We designed a set of species-specific primers for each species targeting a small region of the mitochondrial DNA cytochrome b gene . The distribution of these two species is disjunct from their congeners along the Pacific coast to the west; therefore, we designed primers to be species-specific within our system but also to detect the congeners of each species for wider geographic applicability. Target fragment length was 78 base pairs for Dicamptodon and 85 base pairs for Ascaphus. This test was designed to amplify previously-published sequences characteristic of these species; no new sequence data was generated that had not already been published. All extractions and PCR set-up were done in a room dedicated to low-quantity DNA sources; no DNA from amphibians had previously been handled in this room. Using filter samples taken from stream water, we developed an efficient protocol for detecting targeted DNA sequences for two secretive amphibian species, demonstrating that the recovery of amphibian DNA from stream water is possible even when amphibian populations are at low densities. The rapid field collection protocol, relatively simple field equipment and low cost make this technique widely applicable to broad-scale inventory and monitoring efforts.