Bacterial　communities　in　water　and　sediments　are　important　decomposers　of　lake　ecosystem.　However,　the　differences　in　bacterial　community　structure　and　biodiversity　in　overlying　water　and　sediments　covered　by　aquatic　plants　such　as　Lotus　in　lake　ecosystems　are　still　poorly　understood.　Here　we　collected　paired　overlying　water　and　sediments　in　the　Baiyangdian　(BYD)　Lake　to　explore　their　characteristics　of　bacterial　community.　Our　results　showed　that　bacterial　diversity　indices　such　as　Sobs,　Shannon,　Simpsoneven　and　Phylogenetic　diversity　in　sediment　samples　were　significantly　higher　than　those　in　overlying　water　samples,　which　were　mainly　affected　by　ofloxacin　(OFL),　dissolved　oxygen　and　pH　in　the　overlying　water,　while　norfloxacin　(NOR),　OFL　and　sulfapyridine　(SPD)　in　sediments.　Dominant　phyla　across　all　overlying　water　samples　were　Actinobacteriota　(36.65%),　Proteobacteria　(29.12%)　and　Patescibacteria　(17.01%),　while　Proteobacteria　(20.97%),　Chloroflexi　(19.56%)　and　Actinobacteriota　(13.37%)　in　all　sediment　samples.　Source　Tracker　results　showed　that　about　6.59　±　1.9%　of　the　variations　in　bacterial　community　in　sediments　could　be　attributed　to　the　contribution　of　the　overlying　water　bacterial　community,　which　is　higher　than　that　of　sediments　to　the　overlying　water　bacterial　community.　The　dominant　factors　shaping　the　bacterial　communities　in　the　overlying　water　were　NOR,　dissolved　organic　carbon　(DOC)　and　total　phosphorus,　while　in　sediments　were　NOR,　OFL　and　DOC.　It　is　suggested　that　antibiotics　(especially　NOR)　may　have　a　substantial　effect　on　bacterial　community　rather　than　interaction　of　environmental　compartments　(overlying　water　and　sediments),　and　would　help　to　improve　the　understanding　of　bacteria　transfer　and　coalescence　in　a　shallow　lake　ecosystem.　©　2023　European　Regional　Centre　for　Ecohydrology　of　the　Polish　Academy　of　Sciences