Elevated stream temperature is a primary factor limiting the coho salmon (Oncorhynchus kisutch) population in California\textquoterights Shasta River Basin. Understanding the mechanisms driving spatial and temporal trends in water temperature throughout the Shasta River is critical to prioritizing river restoration efforts aimed at protecting this threatened species. During the summer, the majority of streamflow in the Shasta River comes from large-volume, cold-water springs at the head of the tributary Big Springs Creek. In this study, we evaluated the initial character of this spring water, as well as the downstream fate and transport of these groundwater inflows during July and August 2008. Our results indicated that Big Springs Creek paradoxically provided both cool and warm waters to the Shasta River. During this period, cool groundwater inflows heated rapidly in the downstream direction in response to thermal loads from incoming solar radiation. During the night time, groundwater inflows did not appreciably heat in transit through Big Springs Creek. These diurnally varying water temperature conditions were inherited by the Shasta River, producing longitudinal temperature patterns that were out of phase with ambient meteorological conditions up to 23 km downstream. Findings from this study suggest that large, constant temperature spring sources and spring-fed rivers impart unique stream temperature patterns on downstream river reaches that can determine reach-scale habitat suitability for cold-water fishes such as coho salmon. Recognizing and quantifying the spatio-temporal patterns of water temperature downstream from large spring inflows can help identify and prioritize river restoration actions in locations where temperature patterns will allow rearing of cold-water fishes.