The Polar marginal ice zones are characterized by the complex interaction of ocean, ice, and atmosphere. The associated physical processes take place on different spatial and temporal scales that shape the ecosystem at and underneath the ice. However, the influence of small scale physical processes on biological production is still poorly understood. To investigate the ecologic relations at a marginal ice zone, an autonomous underwater vehicle was deployed. The vehicle was specifically equipped with instruments collecting physical, chemical, and biological data. Dives were conducted between 0 and 50 m water depth, thus covering the entire euphotic zone. Measurements of the vehicle were complemented by means of ship, satellite, and model based data. The vehicle was deployed between Greenland and the Svalbard archipelago; close to the Molloy Deep in the marginal ice zone of the Fram Strait. The results of a dive at a meltwater front that was located several kilometers from the ice edge, indicated wind-driven, vertical transport processes in the water column. These processes featured meso- and submesoscale dimensions. The water column was divided into four different zones characterized by different biogeochemical parameters. The spatial distribution of these parameters (concentration of nitrate and chlorophyll a, oxygen saturation) was patchy; however a specific qualitative ratio was always maintained between the parameters. High chlorophyll a concentrations were associated with high oxygen saturation and low nitrate values (and vice versa). The mesoscale transport process was caused by the wind-driven movement of an ice tongue 70 km in length. The drift of the tongue entailed elevated nitrate levels at the surface (with respect to a similar dive from the previous year). However, no indications for an ecologic response such as increased production rates could be detected thus suggesting that upwelling has occurred shortly before the dive. Enhanced chlorophyll a concentrations in a 2 – 3 km wide “belt” along the front were caused by accumulation processes rather than by primary production. Submesoscale transport processes were caused by wind interacting with the meltwater front and subsequently intensifying the front (frontogenesis). Frontogenetic processes led to water column instabilities and stimulated the formation of an ageostrophic secondary circulation (ASC). The ASC could be identified by upward and downward bulged isopycnals respectively. Additionally, submerging surface water masses could be identified by their chemical and biological signatures. The depth over which the ASC-related circulation penetrated was within the euphotic zone. Thus, the possible ecologic relevance of frontogenetic processes remained unclear. In order to conduct these studies, biogeochemical instruments and supporting systems were integrated into the vehicle. In total, the vehicle is able to measure nine independent parameters (conductivity, temperature, pressure, concentration of nitrate, oxygen and CO2, fluorescence of chlorophyll a and colored dissolved organic matter, and photosynthetically active radiation) and to collect up to 22 water samples. To record the data and to centrally provide the payload with electric power, a payload control computer was integrated into the vehicle. For data processing and correcting the vehicle´s navigation data, newly developed algorithms were applied. Thus, biogeochemical measurements were georeferenced as precise as possible. Methodically, the float maneuver, with the vehicle repeatedly deactivating its thruster and slowly drifting towards the surface, was developed to investigate the stratification of the upper water column. Methods to handle the vehicle´s small-volume water samples were also investigated and suitable procedures were defined. The first studies of this thesis describe the technical foundation of AUV operations focusing on ecological research in MIZs. Following this, the scientific results are presented. Reviewing the achievements of this thesis, open scientific questions and possible technological upgrades are presented in the Outlook section.