Freshwater resources play a central role in social and economic development of modern civilisations, yet their value is often underestimated and neglected in developed countries. In fact, freshwater habitats are facing unprecedented threat because of human activities, and it is necessary to provide reliable water quality indicators to monitor the response of aquatic systems. In this context, remote sensing has a great potential to provide a complementary source of data for monitoring and under-standing the processes involved in inland waters around the world at fine temporal and spatial reso-lutions. The scientific approach adopted in this thesis is based on the integration of complementary sources of information provided by state-of-the-art monitoring methods to foster our understanding of freshwater habitats. Specifically, we demonstrate the additional value provided by combining com-plementary sensors with bio-geochemical measurements and hydrodynamic models, using a rare event in Lake Geneva which got a wide public attention in local newspapers: a calcite precipitation event. The principal focus of the remote-sensing community has recently been directed towards very turbid waters in order to address the challenges involved with the retrieval of mixed constituent concentra-tions. In this thesis, I highlight some important challenges relative to clearer waters which also re-quire further attention from the community. Specifically, I provide a solution to account for vertical non-uniformities of water constituent concentrations using simple approximation models in Lake Geneva. Finally, I provide a comprehensive comparison between state-of-the-art atmospheric correction methods, which are presumably relevant for inland water monitoring and applicable to the new con-stellation of remote sensors. The aim is to provide reliable recommendations to help forthcoming studies to apply the most suited procedure to their investigation.