Beaver dams alter channel hydraulics which in turn change the geomorphic templates of streams. Variability in geomorphic units, the building blocks of stream systems, and water temperature, critical to stream ecological function, define habitat heterogeneity and availability. While prior research has shown the impact of beaver dams on stream hydraulics, geomorphic template, or temperature, the connections or feedbacks between these habitat measures are not well understood. This has left questions regarding relationships between temperature variability at different spatial scales to hydraulic properties such as flow depth and velocity that are dependent on the geomorphology. We combine detailed predicted hydraulic properties, field-based maps with an additional classification scheme of geomorphic units, and detailed water temperature observations throughout a study reach to demonstrate the relationship between these factors at different spatial scales (reach, beaver dam complexes, and geomorphic units). Over a three-week, low flow period we found temperature to vary 2 °C between the upstream and downstream extents of the reach with a net warming of 1 °C during the day and a net cooling of 0.5 °C at night. At the beaver dam complex scale, net warming of 1.15 °C occurred during the day with variable cooling at night. Regardless of limited temperature changes at these larger scales, the temperature variability within a beaver dam complex reached up to 10.5 °C due to the diversity of geomorphic units. At the geomorphic unit scale, the highly altered flow velocity and depth distributions within primary geomorphic units provide an explanation of the temperature variability within the dam complex and insight regarding increases in habitat heterogeneity.