Lake　Villarrica,　one　of　Chile’s　main　freshwater　water　bodies,　was　recently　declared　a　nutrient-saturated　lake　due　to　increased　phosphorus　(P)　and　nitrogen　(N)　levels.　Although　a　decontamination　plan　based　on　environmental　parameters　is　being　established,　it　does　not　consider　microbial　parameters.　Here,　we　conducted　high-throughput　DNA　sequencing　and　quantitative　polymerase　chain　reaction　(qPCR)　analyses　to　reveal　the　structure　and　functional　properties　of　bacterial　communities　in　surface　sediments　collected　from　sites　with　contrasting　anthropogenic　pressures　in　Lake　Villarrica.　Alpha　diversity　revealed　an　elevated　bacterial　richness　and　diversity　in　the　more　anthropogenized　sediments.　The　phylum　Proteobacteria,　Bacteroidetes,　Acidobacteria,　and　Actinobacteria　dominated　the　community.　The　principal　coordinate　analysis　(PCoA)　and　redundancy　analysis　(RDA)　showed　significant　differences　in　bacterial　communities　of　sampling　sites.　Predicted　functional　analysis　showed　that　N　cycling　functions　(e.g.,　nitrification　and　denitrification)　were　significant.　The　microbial　co-occurrence　networks　analysis　suggested　Chitinophagaceae,　Caldilineaceae,　Planctomycetaceae,　and　Phycisphaerae　families　as　keystone　taxa.　Bacterial　functional　genes　related　to　P　(phoC,　phoD,　and　phoX)　and　N　(nifH　and　nosZ)　cycling　were　detected　in　all　samples　by　qPCR.　In　addition,　an　RDA　related　to　N　and　P　cycling　revealed　that　physicochemical　properties　and　functional　genes　were　positively　correlated　with　several　nitrite-oxidizing,　ammonia-oxidizing,　and　N-fixing　bacterial　genera.　Finally,　denitrifying　gene　(nosZ)　was　the　most　significant　factor　influencing　the　topological　characteristics　of　co-occurrence　networks　and　bacterial　interactions.　Our　results　represent　one　of　a　few　approaches　to　elucidate　the　structure　and　role　of　bacterial　communities　in　Chilean　lake　sediments,　which　might　be　helpful　in　conservation　and　decontamination　plans.　©　2023,　The　Author(s),　under　exclusive　licence　to　Springer　Science+Business　Media,　LLC,　part　of　Springer　Nature.