In a time of rising concern about climate change and pollution, the water quality of large lakes acts as an indicator of the health of the environment. To study the water quality at a large scale - up to several hundreds of kilometres - hyperspectral remote sensing is emerging as the main solution. Indeed, different quantities relevant to water quality, like turbidity or concentratrion in chlorophyll-a, can be measured using the spectral reflectance of the water column. Additionally, airborne and spaceborne sensors can cover large areas, thus allowing to study the water at a much larger scale than when simply taking water samples at specific points. Airborne hyperspectral imaging, in particular, offers an acceptable ground resolution - around a metre - which allows to map relevant quantities precisely. However, few existing projects deliver maps that have both a sufficient ground resolution and a large coverage. Furthermore, most existing sensors do not offer a fine spectral resolution, which is for instance crucial when studying the presence of chlorophyll-a, which can only be detected in a narrow range of the electromagnetic spectrum. This thesis presents our work with a hyperspectral sensor developed and used by the Geodetic Engineering Laboratory of EPFL in the Léman-Baïkal project, a cooperative work which aimed at studying both Lake Geneva (Switzerland) and Lake Baikal (Russia). The project included ultralight plane flights with an onboard pushbroom scanner, which allowed to collect data over large areas with a fine spectral resolution. Alongside the use of this sensor came problematics which are at the centre of this thesis: the georeferencing of the scan lines, their radiometric calibration, their analysis and the softwaremanagement of this data. In the following, we present a new method to georeference pushbroom scan lines that uses co-acquired frame images to perform coregistration and to achieve a georeferencing, which RMSE is up to 20 times smaller than the direct one. We propose an efficient radiometric self-calibration method to convert the sensor output to water-leaving reflectance; this method makes use of the visible peaks of atmospheric absorption to align the spectral bands with those of a reference acquisition, and uses the near infrared properties of deep water and vegetation to performabsolute calibration. The last part of the processing - the software management, including data compression - was solved by developing a software called HYPerspectral Orthorectification Software (HypOS). This software is the synthesis of our work, including the tools to performgeometric correction, radiometric calibration and data compression of our hyperspectral data. Two examples of applications are given: the first one deals with mapping chlorophyll-a in the Rhone Delta of Lake Geneva; the second, at a larger scale, uses satellite data to monitor ice coverage over large lakes like Onega or Ladoga (Russia).