The work presented here deals with continental hydrosystem modelling for sustainable management of water resources. It aims at better understanding the hydrological cycle, stream-aquifer interfaces functioning, as well as the anthropogenic impacts on water quality (agricultural practices, urban effluents). Understanding the temporal and spatial variations of piezometric heads is a prerequisite to achieve a sustainable water management. First piezometric head spatial distribution are estimated using various interpolation techniques. Afterwards they are used to perform an automatic calibration of the diffusivity equation. Based on an extensive literature review on multi-parameter optimization and inverse problem, a pragmatic hybrid fitting method that couples manual and automatic calibration is developed for Distributed Process Based Models (DPBMs) of hydrosystems. Three independent data subsets are used for calibration (10 yr), validation (10 yr) and test (35 yr). The fitted DPBM, coupled with a linear model of co-regionalization, is then used to quantify the hydrosystem water mass balance between 1974 and 2009 on the Loire bassin, indicating that the aquifer system is slightly over-exploited. Recent developments in hydrological modelling are based on a view of the stream-aquifer interface being a single continuum through which water flows. These coupled hydrological-hydrogeological models, emphasizing the importance of the stream-aquifer interface, are more and more used in hydrological sciences for pluri-disciplinary studies aiming at questioning environmental issues. We first define the concept of nested stream-aquifer interfaces as a key transitional component of continental hydrosystem. Based on a literature review, we then demonstrate the usefulness of the concept for the multi-dimensional study of the stream-aquifer interface, with a special emphasis on the stream network which is identified as the key component for scaling hydrological processes occurring at the interface. Finally we focus on the stream-aquifer interface modelling at different scales, with up-to-date methodologies and give some guidances for interdisciplinary approaches that couple multi-dimensional monitoring and modelling of the interface. Finally water quality models are investigated based on the river continuum concept that considers community centered models. The ProSe model is used to simulate the Seine river from Paris City to the entrance of the estuary. It appears that hydro-sedimentary processes are of primary importance with regards to the biogeochemical functioning of the river. The influence of stream-aquifer interfaces on biogeochemical fluxes grows even more further upstream. Finally, geostatistics is used to reduce DPBM uncertainties when assessing nitrate concentrations. Mismatches between simulated and observed variograms are analysed as (i) wrong quantification of inputs to the river and (ii) wrong description of physical processes within the river.
