Recent decades have seen unprecedented loss of global biodiversity with amphibians among the most affected species. Emerging infectious diseases have being linked to declines and may result in very rapid extinctions, with chytridiomicoses and ranaviroses cited as diseases with the greatest impact. However, demonstration of a link between population declines and infectious pathogens is not always straightforward and becomes harder if pre-outbreak data are not available. With this thesis I combine observational, experimental and modelling approaches to analyse the spread and impacts of emerging agents on amphibian assemblages. In Iberia, the first case of Bd-infection and consequent mass mortality was documented in 1997 in Sierra de Guadarrama (Spain), leading to the decline of common midwife toads (Alytes obstetricans). In Portugal, impacts were first recorded in 2009 in Serra da Estrela and here described. Bd led to a collapse of midwife toads in high altitude areas. However, despite being regarded as a highly susceptible host to Bd, midwife toads seem to exhibit strong variation in the prevalence of infection across small geographic scales. Although present at lower elevations, an altitudinal envelope prevented chytrid from causing mortality among this amphibian assemblage. Through ongoing monitoring, I detected the asynchronous emergence of a second pathogen: a Ranavirus. The new virus had the capacity to infect multiple hosts, leading to massive annual die-offs in different taxa, life stages and across the altitudinal range. Data recorded prior to the first outbreak, as well as observations at a comparable site with similar geoclimatic features, illustrated the collapse of the amphibian community in relation to potential drivers. Laboratory experiments and field observations showed that S. salamandra larvae were resistant to the disease chytridiomycosis despite sharing Bd-positive sites with dying Alytes. These results contrast with other higher elevation systems where salamander larvae often overwinter. This prolonged exposure increases the chances of infection and supports the idea that the impact of a pathogen can be mediated by host life history. The mediation of a pathogen impact by the host natural history and/ or particular behaviour was also demonstrated on newts. The lethal effects of Ranavirus annual exposure on the newt population were amplified by host phenology causing a strongly imbalanced adult sex ratio. Modelling showed how behaviour may influence recovery. Following mass mortality, population recovery will be faster if there is an even sex ratio. Bd-mediated declines and extinctions may occur in species with certain life history traits, whereas Ranavirus CMTV-like strains seem to have a broader impact across amphibian species. Good surveillance and monitoring are key steps for effective management and conservation of wild populations. Sustainable conservation of wild amphibian assemblages is dependent on long-term population persistence and co-evolution with these lethal pathogens.