A greater understanding of eDNA behavior in the environment is needed before it can be employed for ecosystem monitoring applications. The objectives of this study were to use autonomous sampling to conduct long‐term, high‐frequency monitoring of the eDNA of native salmonid species in a Californian coastal stream, describe temporal variation of eDNA on multiple scales and identify environmental factors that drive this variation, and evaluate the ability of the eDNA datasets to detect rare species and represent organismal abundance. Using high‐throughput autonomous environmental sample processors (ESPs) and qPCR, we enumerated eDNA concentrations from 674 water samples collected at subdaily intervals over 360 days at a single site. We detected eDNA from two imperiled salmonids (coho salmon Oncorhynchus kisutch and steelhead/rainbow trout O. mykiss) in most samples; O. kisutch eDNA was generally in lower concentration and more variable than O. mykiss eDNA. High‐frequency (i.e., subdaily and daily) variability in salmonid eDNA concentrations showed occasional patchiness (i.e., large differences between consecutive samples), while seasonal differences were observed consistent with the ecology of the species at this site. Salmonid eDNA concentrations were significantly associated with creek discharge, photoperiod, and whether the creek mouth was open or closed by a seasonal sandbar. The release of hatchery‐origin O. kisutch parr into the stream was associated with a significant increase in eDNA concentration for the remainder of the study. We compared eDNA signals with fish abundance data collected from traps located at the site. Fish were detected more often by eDNA than from trapping. Significant positive associations between fish abundance and eDNA concentrations were observed for O. mykiss; however, no such associations were observed for O. kisutch. This study adds to our knowledge on the occurrence and behavior of fish eDNA in lotic systems and informs future biomonitoring efforts using automated sampling technology.