Few genomic and metagenomic studies have focused on freshwater systems in the last years. Most of the studies carried out on these particular environments so far rely on microscopy, physiology, phenotypic observations, individual genes and 16S rRNA sequencing. Here, we shed light on microbial communities from oligotrophic and mesotrophic freshwater systems using high-throughput deep sequencing metagenomics and genome-resolved metagenomics. We have focused on the study of ubiquitous and cosmopolitan microbial groups from two temperate Spanish reservoirs (Tous, Amadorio). Among these, we studied freshwater picocyanobacteria from Synechococcus and Cyanobium genera, which so far have not been well characterized at the genomic level, compared to the marine representatives. In particular, we were able to isolate two of the most abundant picocyanobacteria from Tous reservoir, which were previously studied via metagenomics. These picocyanobacteria are not only abundant in this reservoir but are widely distributed in different freshwater and brackish systems. In this work we also shed light on some of the first freshwater representatives of the phylum Verrucomicrobia, that are ecologically uncharacterized in freshwater systems about which relatively little is known. We discovered a wide range of metabolisms in these microbes, ranging from nitrogen fixation and photoheterotrophy via rhodopsin pumps to important contributions in the degradation of recalcitrant matter and polysaccharides. We also include the first metagenomic study of the microbial communities under the ice waters of the largest (by volume) ultraoligotrophic lake in the world, Lake Baikal. This study has provided a first glimpse and a particular microbial composition on the sub-ice, having found an unusual fraction of Verrucomicrobia and new microbial lineages from many typical freshwater phyla, including the first freshwater representative of the groups I/II of SAR11 lineage and novel genomes of Proteobacteria, Thaumarchaeaota, Gemmatimonadetes, Cyanobacteria, Planctomycetes, Bacteroidetes, Acidobacteria, Nitrospirae, Verrucomicrobia or Actinobacteria.