Temporal stability of ecosystem functions is often regulated by the same environmental factors that also shape diversity. Therefore, species diversity, ecosystem functions and their environmental regulators should be considered together to understand and predict the consequences of anthropogenic disturbances on ecosystems. We studied the influence of land-use disturbance (agriculture) and a natural stressor (low pH due to specific geology) on the temporal variability (variability among successive years) of fungal decomposer communities and leaf decomposition rates in streams. We used next-generation sequencing techniques (pyrosequencing) to determine the composition of fungal assemblages. Temporal variability of leaf decomposition was higher in human-disturbed streams than in circumneutral reference or naturally acidic sites, whereas the latter two did not differ. Fungal operational taxonomic unit (OTU) richness and evenness were lower in human-impacted sites than in circumneutral reference sites. However, there were no significant differences between stream types in the temporal variability of fungal community composition. Fungal OTU evenness was negatively and among-year variability of water chemistry positively related to temporal variability in leaf decomposition. Partial regressions showed that these two factors had independent effects on decomposition rates. Although the dominant OTUs in the disturbed streams were temporally stable, they did not maintain stable ecosystem functions, suggesting that variability in decomposition was driven mainly by changes in the metabolic responses of dominant taxa to environmental fluctuations. Our results show that leaf decomposition rates in reference sites vary little through time, supporting the use of leaf decomposition assays in bioassessment. Our results also highlight the importance of measuring not only the mean rates, but also temporal variability of process rates when assessing the influence of human disturbance on ecosystem functioning.