Methods describing how to sample aquatic and semiaquatic amphibians in small streams and headwater habitats in the Pacific Northwest are presented. We developed a technique that samples 10-meter stretches of selected streams, which was adequate to detect presence or absence of amphibian species and provided sample sizes statistically sufficient to compare abundance of individual species among streams. Physical and biological parameters of stream are described as well as ways to collect amphibians effectively. The system can be modified for use in a variety of waterways and for different study objectives. We provide recommendations for improvements on future studies.