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Carbon cycling in headwater streams is mostly driven by the decomposition of allochthonous organic matter, and to a lesser extent by primary production. Quantifying the influence of temperature on these processes is therefore essential to better anticipate the consequences of global warming for stream ecological functioning. In this study, we measured alder litter microbial decomposition and associated fungal biomass and diversity, using leaf discs enclosed in fine-mesh bags along a natural geothermal temperature gradient, in both spring and winter. We monitored the chlorophyll-a accrual in biofilms growing on ceramic tiles. The temperature gradient, from upstream to downstream, ranged from 15.3 to 14.2 degrees C in spring and 18.2 to 13.2 degrees C in winter. Autotrophs and heterotrophs exhibited contrasting responses to temperature. The expected positive effect of temperature was actually observed for chlorophyll-a accrual only, while an apparent temperature-independence of litter decomposition rate was found. Moreover, temperature effects on heterotrophic and autotrophic organisms depended on the season, with higher litter decomposition rates, sporulation rates, fungal biomass and chlorophyll-a in spring, despite a lower mean water temperature than in winter. Together, these results suggest that the influence of temperature remained largely overrode by seasonal effects. This result is likely due to annual variations in light availability, and may involve indirect positive interactions between microbial primary producers and decomposers.