Ecological　floating　beds　can　rapidly　remove　nutrients　(nitrogen　and　phosphorus)　from　eutrophic　water,　but　we　still　know　little　about　whether　this　process　can　simultaneously　recover　microbial　eukaryotic　communities.　To　fill　this　gap,　planktonic　microbial　eukaryotic　communities　were　investigated　using　18S　rRNA　high-throughput　gene　sequencing　during　nutrient　removal　by　floating　beds　of　Canna　indica　L.　We　found　that　nutrient　concentrations　were　high　in　both　the　control　and　treatment　groups　during　period　1　(days　0–5)　but　rapidly　decreased　in　the　treatment　group　during　period　2　(days　6–9)　and　period　3　(days　10–18).　However,　the　microbial　eukaryotic　species　richness　and　community　compositions　were　similar　between　the　control　and　treatment　groups　during　periods　1　and　2　but　showed　small　differences　during　period　3.　The　microbial　eukaryotic　co-occurrence　networks　between　the　control　and　treatment　groups　also　showed　similar　degree　centrality　and　interconnected　eukaryotic　members.　We　found　that　some　abundant　fungi　species　significantly　responded　to　nutrient　variations,　but　a　large　number　of　abundant　ciliates　were　insensitive　to　nutrient　removal.　Our　findings　suggest　that　ecological　floating　beds　can　rapidly　remove　nutrients　in　eutrophic　waters　but　that　it　is　difficult　to　quickly　and　simultaneously　improve　microbial　eukaryotic　communities.　This　result　reveals　the　critical　influence　of　nutrient　pollution　on　aquatic　ecosystems　and　therefore　on　long-term　and　comprehensive　aquatic　habitat　restoration,　as　aquatic　macrophyte　recoveries　should　be　conducted　after　nutrient　controls　have　been　implemented.　©　2019　Elsevier　B.V.