AbstractDespite the importance of thermal conditions in influencing biodiversity of alpine river systems, knowledge of year round stream temperature variability is very limited. This paper advances understanding of alpine stream temperature dynamics using hourly resolution data collected over two consecutive years at five sites within a glacierized basin in the French Pyrénées. The potential utility of temperature for understanding river flow patterns at ungauged sites (most notably during winter) is explored. The results indicated marked heterogeneity in water column temperatures; groundwater streams were typically warmer and more thermally stable than those draining snow and ice. Based upon stream temperature patterns, it appears possible to differentiate between river flow conditions including: free‐flowing, surface freezing, dewatering and snow cover. Notably, groundwater‐fed streams appeared to exhibit greater flow permanency than meltwater‐fed streams, the latter freezing for extended periods. These new insights into long‐term alpine stream thermal conditions have major implications for understanding the strategies adopted by benthic macroinvertebrate taxa when overwintering, particularly where streams freeze. Copyright © 2006 John Wiley & Sons, Ltd.