We investigated the aquatic and riparian herpetofauna in a 789 km2 river catchment in northwest California to examine competing theories of biotic community structuring in catchment stream networks. Research in fluvial geomorphology has resulted in multi‐scale models of dynamic processes that cyclically create, maintain, and destroy environments in stream networks of mountain catchments. These models have been applied to understanding distributions of invertebrates, algae, fishes and their habitats across entire basin networks, but similar approaches with herpetofauna are rare. We examined multi‐scale spatial patterns of multiple species as they related to variation in channel types, channel settings, and within‐channel attributes that result from these processes. From 83 reaches distributed randomly throughout the watershed, we distinguished four channel types: 1) high gradient with cascade structure; 2) 2–4% gradient with step‐pool structure controlled by moderately steep valleys; 3) slightly entrenched, lower gradient, plane‐bed structure; and 4) low gradient, shallow, unconfined, multiple or migrating pool/riffle channels in broad alluvial valleys. The composition of herpetofauna differed in five of six pair‐wise comparisons among these channel types, indicating a minimum of three distinct mesoscale assemblages. We used non‐parametric multiple regression (NPMR) to examine relationships at multiple spatial scales. NPMR revealed species‐specific associations with channel settings and within‐channel environments among species sharing the same sets of channel types. Morphological adaptations, biophysical limits and natural histories of each species best explained their associations with distinct sets of attributes surrounding and within channel types. While each set of species has similarly adapted to fluvial and geomorphic disturbance processes structuring channels at the mesoscale, species within each set have adapted to a unique set of attributes that are best discerned when their spatial relationships are examined across multiple spatial scales. We evaluated the various spatial patterns against hypotheses of stream community organization and metacommunity perspectives.