Accurate assessments of fish populations are often limited by re-observation or recapture events. Since the early 1990s, passive integrated transponders (PIT tags) have been used to understand the biology of many fish species. Until recently, PIT applications in small streams have been limited to physical recapture events. To maximize recapture probability, we constructed PIT antenna arrays in small streams to remotely detect individual fish. Experiences from two different laboratories (three case studies) allowed us to develop a unified approach to applying PIT technology for enhancing data assessments. Information on equipment, its installation, tag considerations, and array construction is provided. Theoretical and practical definitions are introduced to standardize metrics for assessing detection efficiency. We demonstrate how certain conditions (stream discharge, vibration, and ambient radio frequency noise) affect the detection efficiency and suggest that by monitoring these conditions, expectations of efficiency can be modified. We emphasize the importance of consistently estimating detection efficiency for fisheries applications.