The study of exoplanet atmospheres is essential to understand the formation, evolution and composition of exoplanets. When a planet pass between its host star and an observer, a fraction of the star-light is absorbed by its atmosphere, thus revealing its composition. This thesis focuses on the use of high-resolution spectrographs to extract unambiguously atmospheric signals and learn more about the dynamic and composition of exoplanet atmospheres. Two atmospheric tracers have particularly been studied, the helium triplet and the visible water vapor bands. They provide complementary information on the atmospheric structure. This thesis also explores how instrumental systematics and the Earth contamination impact high-resolution spectra and how it is possible to remove them. Finally, this work describes the construction of atmospheric surveys for state-of-the-art high-resolution spectrographs, such as ESPRESSO and NIRPS. These surveys will provide a robust and statistical view of exoplanet atmospheres.