Nutrient　(nitrogen　and　phosphorus)　removal　by　using　bioremediation　technologies　in　eutrophic　water　alters　bacterial　and　protist　community　structure　and　function,　but　how　it　changes　the　stability　of　community　remains　unclear.　To　fill　this　gap,　in　this　study,　bacterial　and　protist　communities　were　investigated　using　16S　and　18S　rRNA　gene　high-throughput　sequencing　during　the　nutrient　removal　by　using　ecological　floating　beds　of　Canna　indica　L.　Our　results　showed　that　both　bacterial　and　protist　community　compositions　in　the　treatment　group　were　similar　to　those　in　the　control　group　at　the　beginning　of　the　experiment　(day　1　to　day　11),　but　then　bacterial　and　protist　community　compositions　became　more　stable　with　the　removal　of　nutrients　in　the　treatment　group　than　those　in　the　control　group　(day　12　to　day　18).　We　further　explored　the　mechanisms　for　this　increased　stability　and　found　that　the　contribution　of　the　stochastic　process　to　bacterial　and　protist　community　variations　was　higher　in　the　control　group　than　that　in　the　treatment　group.　This　suggests　that　the　high　nutrient　concentration　in　the　control　group　might　increase　the　random　colonization　or　extinction,　and　therefore　resulted　in　the　high　temporal　variability　(i.e.,　unstable)　of　bacterial　and　protist　communities.　Our　findings　suggest　that　bioremediation　for　eutrophication　can　promote　the　stability　of　aquatic　communities,　and　therefore　potentially　maintain　aquatic　ecosystem　functions　and　services　to　humanity.　©　2021,　The　Author(s),　under　exclusive　licence　to　Springer　Science+Business　Media,　LLC,　part　of　Springer　Nature.