Mountain freshwater ecosystems provide essential services to humanity, such as the provision of clean water, but are strongly affected by anthropogenic global change despite their apparent isolation. Benthic biofilms, communities of organisms living in a matrix adhering to submerged surfaces, have critical functions in mountain lakes: among others, they detoxify water and form the basis of food webs. However, their composition and biodiversity are still poorly understood. Also, in the Pyrenees, some amphibian populations are threatened by chytridiomycosis, an infectious disease caused by the zoosporic fungus Batrachochytrium dendrobatidis (Bd). Its epidemiology is not fully understood but may depend on biofilms, which are abundant in mountain lakes and form the food of tadpoles. Here, I had two main objectives: first, to study the spatio-temporal variations of biofilm microbial biodiversity; second, to investigate the potential role(s) of biofilms in the epidemiology of Bd infections. To do this, I performed a metataxonomic analysis of the prokaryotic and microeukaryotic assemblages of 230 biofilm samples collected from 2016 to 2020 in 26 Pyrenean mountain lakes. Combining this with Bd infection data from tadpoles sampled in the same lakes, I explored the links between the microbial composition of biofilms and the distribution, frequency and population impacts of Bd infections. In the laboratory, I also tested whether a biofilm could affect the free-living, infectious stage of Bd, the zoospore. My hypotheses were that the biodiversity of biofilms would decrease and their assemblages would change over the course of the study, that biofilms from lakes with less infected/impacted amphibian populations would contain more Bd antagonists than biofilms from other lakes, and that biofilms produced in the laboratory would not affect the number of zoospores unless they contained Bd consumers. The diversity in both prokaryotic and micro-eukaryotic biofilm assemblages decreased over the study period. Their compositions also changed over the five years, with an increase in cyanobacteria (possibly toxigenic organisms) in prokaryotes and a decrease in diatoms (indicator organisms) in micro-eukaryotes. Taken together, these results show that benthic biofilm communities are degrading with potentially negative implications for the entire aquatic ecosystem and water quality. In addition, I found that biofilms in lakes where amphibians are less infected and less impacted by Bd had a higher abundance of Bd-inhibiting or Bd-consuming organisms. Finally, I showed that biofilms, even when they do not contain Bd consumers but only a phototrophic alga, can affect Bd zoospores by inactivating them or forcing them to immobilise. My transdisciplinary research illustrates the interactions between environmental health and animal and public health. Contemporary environmental changes are deteriorating biofilms, the very basis of food webs in mountain lakes. This is likely to have profound cascading effects on mountain socio-ecosystems as a whole, such as a potential increase in the risk of Bd infection and chytridiomycosis for amphibians, and cyanotoxicosis for all vertebrates that frequent mountain lakes, including humans and livestock. If mountain freshwater ecosystems are to continue to provide services rather than disservices, the factors contributing to biofilm change will need to be rapidly identified and mitigated.