In the period 2009–2011, the micromycetes causing symptoms on the leaves of <em>Schoenoplectus lacustris</em> (SL) from Płociczno and Płociowe lakes in Drawa National Park (DNP) were investigated. A total of 39 taxa of microscopic fungi and chromistan fungi were found. The taxonomic structure of the mycobiota was dominated by anamorphs of Ascomycota. In each year of the study, the SL fungal species richness was higher in Płociowe Lake than in Płociczno Lake. In all the years of study in both lakes, the fungal community on SL was composed of the following six dominant species: <em>Alternaria alternata</em>, <em>Cladosporium herbarum</em>, <em>Fusarium incarnatum</em>, <em>F. sacchari</em>, <em>Gibberella avenacea</em>, and <em>Pleospora scirpicola</em>. The species occurring exclusively in Płociczno Lake were <em>Papulaspora immersa</em>, <em>Puccinia scirpi</em>, and <em>Trichothecium roseum</em>, and those found only in Płociowe Lake were <em>Acremoniella atra</em>, <em>Alternaria atra</em>, <em>Aspergillus niger</em>, <em>A. versicolor</em>, <em>Fusarium oxysporum</em>, <em>Gonatobotrys simplex</em>, <em>Massariosphaeria scirpina</em>, <em>Microascus brevicaulis</em>, <em>Penicillium chrysogenum</em>, and <em>Stagonospora aquatica</em>. Only one confirmation of the occurrence of <em>Puccinia scirpi</em> and the lack of other specialized obligate parasites indicate the good health of SL in DNP. The facultative parasites, inter alia, <em>Boeremia exigua</em>, <em>Chaetomium globosum</em>, <em>Fusarium culmorum</em>, <em>F. incarnatum</em>, <em>F. sacchari</em>, <em>Gibberella avenacea</em>, and <em>Stagonospora aquatica</em> that are present on plants as part of the natural process of apoptosis may influence the health of SL.