Agrosystems (farming and arable crops) interact strongly with their environment and especially with aquatic and atmospheric systems. Most of these exchanges take place through the water cycle that conveys organic matter, both as a source of nutrients and potential pollutants. This organic matter is transformed by biogeochemical cycles in which microorganisms are particularly involved. Aquatic systems interact with agrosystems through groundwater and rivers, but also through irrigation systems. Agrosystems, sources of aerosols (soil particles, bioaerosols), VOCs (Volatile Organic Compounds) and greenhouse gases will participate in atmospheric processes and affect the formation of clouds and precipitation, which will impact agrosystems. These interactions, which are extremely complex, partly condition the economic and environmental quality of agricultural production, it is essential to better understand the foundations for increasing the performance of agro-systems and towards sustainable agricultural management (efficient and less impacting on the environment). Understanding of these interactions requires a thorough knowledge of the bio-physico-chemical processes in atmospheric and aquatic environments, based on data from observation and experimentation.