Stream temperature was recorded between 2002 and 2005 at four sites in a coastal headwater catchment in British Columbia, Canada. Shallow groundwater temperatures, along with bed temperature profiles at depths of 1 to 30 cm, were recorded at 10‐min intervals in two hydrologically distinct reaches beginning in 2003 or 2004, depending on the site. The lower reach had smaller discharge contributions via lateral inflow from the hillslopes and fewer areas with upwelling (UW) and/or neutral flow across the stream bed compared to the middle reach. Bed temperatures were greater than those of shallow groundwater during summer, with higher temperatures in areas of downwelling (DW) flow compared to areas of neutral and UW flow. A paired‐catchment analysis revealed that partial‐retention forest harvesting in autumn 2004 resulted in higher daily maximum stream and bed temperatures but smaller changes in daily minima. Changes in daily maximum stream temperature, averaged over July and August of the post‐harvest year, ranged from 1.6 to 3 °C at different locations within the cut block. Post‐harvest changes in bed temperature in the lower reach were smaller than the changes in stream temperature, greater at sites with DW flow, and decreased with depth at both UW and DW sites, dropping to about 1 °C at a depth of 30 cm. In the middle reach, changes in daily maximum bed temperature, averaged over July and August, were generally about 1 °C and did not vary significantly with depth. The pre‐harvest regression models for shallow groundwater were not suitable for applying the paired‐catchment analysis to estimate the effects of harvesting. However, shallow groundwater was warmer at the lower reach following harvesting, despite generally cooler weather compared to the pre‐harvest year. Copyright © 2012 John Wiley & Sons, Ltd.