Headwaters, which are the most common stream order in the landscape, are mostly dependent on energy produced in the terrestrial system, largely consisting of leaf litter from riparian vegetation. The aim of this study was to investigate the decomposition in headwaters of leaf litter from three native (alder, birch, spruce) and one non-native (lodgepole pine) species and how decomposition responds to changes in the environment. Further, microbial and shredder influences on leaf-litter decomposition and aquatic decomposer ability to adapt to non-native species was investigated. By using field-data from this study, calculations were made to assess if microbes and shredders are resource limited. Litterbags were placed in 20 headwater streams in northern Sweden that varied in water chemistry, stream physical characteristics and riparian vegetation. The results revealed that species litter decomposition of different plant species was affected differently by changes in environmental variables. Alder and birch decomposition were positively associated, whereas lodgepole pine deviated from the other species in decomposition and its relationship with important environmental variables, indicating that the ability of the boreal aquatic systems to decompose litter differs between introduced and native species. When including macroinvertebrates, shredder fragmentation generally increased decomposition, but was not significant for all sites. Resource availability for microbes and shredders was controlled by litter input, and no risk of resource limitations was evident during the study period. These findings highlight a complexity of the decomposition process that needs to be considered when predicting changes due to human activities.