This thesis explored to types of tropical high-altitude freshwater ecosystems located in Southern Ecuador: shallow paramo lakes and mountain streams. Apart from describing some of their basic characteristics for the very first time, we tested three different aspects of the composition and functioning of ecological systems. First, the biodiversity and ecosystem functioning relationship. Second, the distance-decay hypothesis and third, the impact of the degradation of the surrounding vegetation on stream water condition. This thesis provides a baseline for future studies on the impact of climate change and human activities on tropical high-altitude freshwater lakes. These results suggest that by modifying the abiotic and biotic parameters of tropical high-altitude lakes, human activities can indirectly impact their functioning and their capacity to provide vital ecosystem services. No links were found between geographic distance and phytoplankton composition. On the contrary, some environment related patterns of community structure were observed. Regarding streams, the results report the differences in the water condition according to the type of vegetation in the watershed. Moreover, the diatom communities also responded to changes in land use in the watersheds.