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Summary Recent advances in sequencing technology and bioinformatic pipelines have allowed unprecedented access to the genomes of yet‐uncultivated microorganisms from diverse environments. However, the catalogue of freshwater genomes remains limited, and most genome recovery attempts in freshwater ecosystems have only targeted specific taxa. Here, we present a genome recovery pipeline incorporating iterative subtractive binning, and apply it to a time series of 100 metagenomic datasets from seven connected lakes and estuaries along the Chattahoochee River (Southeastern USA). Our set of metagenome‐assembled genomes (MAGs) represents >400 yet‐unnamed genomospecies, substantially increasing the number of high‐quality MAGs from freshwater lakes. We propose names for two novel species: ‘CandidatusElulimicrobium humile’ (‘Ca. Elulimicrobiota’, ‘Patescibacteria’) and ‘CandidatusAquidulcis frankliniae’ (‘Chloroflexi’). Collectively, our MAGs represented about half of the total microbial community at any sampling point. To evaluate the prevalence of these genomospecies in the chronoseries, we introduce methodologies to estimate relative abundance and habitat preference that control for uneven genome quality and sample representation. We demonstrate high degrees of habitat‐specialization and endemicity for most genomospecies in the Chattahoochee lakes. Wider ecological ranges characterized smaller genomes with higher coding densities, indicating an overall advantage of smaller, more compact genomes for cosmopolitan distributions.