Headwater and intermittent streams have traditionally been considered less biologically diverse than downstream perennial reaches. However, recent studies have highlighted the significant role that headwaters play in supporting regional aquatic biodiversity. Additionally, intermittent streams in the Pacific Northwest may be more diverse than similar streams in other regions. Here, we present a four-year biodiversity study of the John West Fork, an intermittent coastal headwater stream in northern California. It only flows for 5–7 months each year, but supports residual perennial pools during the summer dry season. Our goals are to describe the physical and biological settings of the John West Fork, document its aquatic biodiversity, and promote the use of it and similar streams as study systems. From 2009 to 2012, we sampled fish and invertebrates in riffles and pools during early summer (June) and in residual pools during late summer (late September/early October). We documented four vertebrate species (steelhead trout, coho salmon, California giant salamander, and Pacific chorus frog) and 159 aquatic invertebrate taxa. Steelhead trout were common each year, but coho salmon were present only in 2010 and 2011. Most invertebrate taxa were tolerant of stagnant pool conditions; only nine taxa were exclusive to flowing riffle habitats. Intermittent headwater streams similar to John West Fork are numerous along the west coast of North America. This great number of replicate systems and their tractability make them ideal for ecological studies, and their high biodiversity makes them deserving of consideration in local and regional conservation planning.