Headwater streams are important parts of freshwater ecosystems that control downstream water quality. These streams are characterized by limiting conditions for the development of phototrophic organisms. In these ecosystems, benthic diatoms are the main primary producers but their production represents only a minor fraction of the organic carbon available for higher trophic levels. However, while not quantitatively important, benthic diatoms can play a major role in the functioning of these streams, through secondary production and nutrient recycling. This is due in particular to their production of highly labile (easily degradable and/or consumable by organisms) organic matter for microbial decomposers, but also to their high levels of long-chain polyunsaturated fatty acids, which are essential for macroinvertebrate development. In the context of global change, anthropogenic stressors may impede the development of diatoms, notably by favoring other primary producers such as cyanobacteria and chlorophytes, and therefore have cascading effects on aquatic ecosystems. Firstly, we present an overview of headwater streams, the factors constraining photosynthesis in these ecosystems, and the extent and dynamics of diatom-based organic matter in comparison to other sources. Secondly, we discuss how anthropogenic activities may affect the relative role of diatoms, especially in the case of lowland areas, which are currently poorly studied.