The subalpine and jura middle mountains are composed of a many karstic systems characterized by small size and area. For local towns, these systems can represent the only water resource. The catchment areas are mainly composed of forests and pastures and have a limited urbanisation. Local karst systems have quick flow transfer and are not really known in the region. The main goal of this thesis is the study of the relationship between functioning and vulnerability of middle mountains karst systems. The vulnerabilities are analysed with three approaches: intrinsic, anthropogenic and climatic, applied on eight sites with variable natures (karst spring, karst conduit and rivers) which are additional. The intrinsic vulnerability is studied by the use of PaPRIKa method. This method is based on the overlaying by weighting catchment area maps. Each map is represented by one criterion. Criteria used to carry out a final map are: Rock, Infiltration, Protection and karstification. The method allows the characterization of the vulnerability degrees on the catchment area. Although the study systems have hydrodynamic functioning and similar soil occupation, the vulnerability degrees change for each site. Within the ALPEAU program, the soil remobilization due to sylvicultural activities is used as an anthropogenic vulnerability factor on the catchment area. The study is focused on dissolved and suspended organic matter, especially the fluorescent organic matter. This work has begun with the study of the organic matter transfers during hydrological cycle in natural conditions (without anthropogenic activities). During or after sylvicultural activities, karst waters can show turbidity peaks associated with concentration increasing of humic like, protein like, total nitrogenous and total organic carbon. However, all sites don't show a significant increase in spite of the intensity of sylvicultural activities. The climatic vulnerability is approached with the study of historical data since 60 years. The temporal evolution of precipitation, discharge and temperature have been analysed in order to extract global trends. Besides temperature increase (+15°C) since 50 years, the quantity of precipitations shows a decrease from 1980. This decrease is particularly accentuated since 2003. The decrease of precipitation and the increase of temperature lead an impact on the ground and fresh water quantity. Trends observed on mean annual discharge are correlated with the variation of precipitations. Despite an early snowmelt, low flow periods, defined by the VCN10, don't show significant increase on the period 1960-2011.
