In mountains, environmental gradients are steep in both terrestrial and aquatic systems, and climate change is causing upward shifts of physical and biological features of these gradients. Glacial streams are an interesting system to evaluate such shifts both because streams have a linear nature (for simplicity of analysis), and because the stream habitat will at least temporarily lengthen as it follows receding glaciers upward. The Tschierva Glacier, Swiss Alps, receded 482 m upstream from 1997 to 2008. We tested the null hypothesis that the physical and biological stream gradient below this glacier maintained the same structure between these time periods, but simply shifted upward following the glacial source. We compared longitudinal patterns of water temperature and zoobenthic community structure in 1997 and 2007–2008 during three seasons (spring, summer, fall) along the uppermost ca. 5 stream km. Upward shifts were evident, including colonization of the newly exposed stream reaches by cold-adapted taxa, and the appearance in 2007/2008 of four lower-altitude species that were previously absent. Overall, however, results rejected the null hypothesis, instead revealing significant changes in gradient structures. These included a more steeply increasing temperature profile downstream of the glacier and increased amplitude of seasonal community turnover in 2007/2008 vs. 1997. Long-term (1955–2007) flow records revealed increasing short-term and seasonal hydrologic variability, which might have influenced the increased intra-annual community variability. The steepening of the temperature gradient was likely caused by a warming lake-outlet tributary upon which glacial influence was diminished between 1997 and 2007/2008. These results suggest that upward-shifting gradients in glacial streams can involve complex interactions with other landscape elements and that local-scale climate response can progress even more rapidly than the rate of glacial recession.