Stream bed temperature profiles were monitored continuously during water year 1990 and 1991 (WY90 and 91) in two New Mexico arroyos, similar in their meteorological features and dissimilar in their hydrological features. Stream bed temperature profiles between depths of 30 and 300 cm were examined to determine whether temporal changes in temperature profiles represent accurate indicators of the timing, depth and duration of percolation in each stream bed. These results were compared with stream flow, air temperature, and precipitation records for WY90 and 91, to evaluate the effect of changing surface conditions on temperature profiles. Temperature profiles indicate a persistently high thermal gradient with depth beneath Grantline Arroyo, except during a semi-annual thermal reversal in spring and autumn. This typifies the thermal response of dry sediments with low thermal conductivities. High thermal gradients were disrupted only during infrequent stream flows, followed by rapid re-establishment of high gradients. The stream bed temperature at 300 cm was unresponsive to individual precipitation or stream flow during WY90 and 91. This thermal pattern provides strong evidence that most seepage into Grantline Arroyo failed to percolate at a sufficient rate to reach 300 cm before being returned to the atmosphere. A distinctly different thermal pattern was recorded beneath Tijeras Arroyo. Low thermal gradients between 30 and 300 cm and large diurnal variations in temperature, suggest that stream flow created continuous, advection-dominated heat transport for over 300 days, annually. Beneath Tijeras Arroyo, low thermal gradients were interrupted only briefly during periodic, dry summer conditions. Comparisons of stream flow records for WY90 and 91 with stream bed temperature profiles indicate that independent analysis of thermal patterns provides accurate estimates of the timing, depth and duration of percolation beneath both arroyos. Stream flow loss estimates indicate that seepage rates were 15 times greater for Tijeras Arroyo than for Grantline Arroyo, which supports qualitative conclusions derived from analysis of stream bed temperature responses to surface conditions.