Shallow lakes provide a multitude of ecosystem functions, but they are particularly vulnerable to natural and anthropogenic disturbances. Understanding the driving factors determining the fate and spatial distribution of nutrients and pollutants in such systems is fundamental to assess the impact of ongoing or future external pressures endangering their ecological integrity. This study investigates the fate of trace contaminants transported into the large shallow Lake Neusiedl, including contaminants representative of different patterns of sources and emission pathways and of environmental behavior, namely metals, pharmaceuticals, an artificial sweetener and perfluoroalkyl substances. Further, it examines the horizontal spatial distribution of nutrients, ions and physico-chemical parameters with an unprecedented detailed focus on the internal variability within the large reed belt. As described in the past e.g. for chloride, evaporation was identified as the process leading to a substantial concentration enrichment of the industrial chemical PFOA and the sweetener acesulfame K from the tributary river into the open lake. This is particularly relevant in view of the predicted future increase of evapotranspiration due to climate change. In contrast, the observed loss of diclofenac, but also of PFOS and carbamazepine suggests that the well-mixed, humic-rich and alkaline Lake Neusiedl offers favorable conditions for the photodegradation of otherwise very persistent chemicals. Another important finding, in the context of possible modifications in lake water levels due to climate change, is the fundamental role played by the connectivity between open lake and reed belt but also by the presence and characteristics of inner water areas within the reed belt region in determining the hydrochemistry of the lake system. By revealing systematic spatial patterns and by focusing on the underlying factors and processes, the understanding offered by this study is of high value for the conservation of shallow lakes.