Using sediment samples from theSolthörn tidal flat (southernNorthSea,Germany), collected in bi‐weekly intervals fromJune toJuly 2012, a range of qualitative and quantitative screening methods for oomycete and chytrid pathogens infecting benthic diatoms were evaluated. Pre‐treatment of sediment samples using short ultrasound pulses and gradient centrifugation, in combination withCalcoFluor White, showed the best results in the visualization of both pathogen groups. The highest number of infected benthic diatoms was observed in midJuly (5.8% of the total benthic diatom community). Most infections were caused by chytrids and, in a few cases, oomycetes (LagenismaDrebes (host:Coscinodiscus radiatusEhrenberg) andEctrogellaZopf (hosts:Dimeregramma minorinPritchard andGyrosigma peisonis). Among the chytrids, sporangium morphology indicated the presence of five different morphotypes, infecting mainly epipelic taxa of the ordersNaviculales (e.g.,Navicula digitoradiata) andAchnanthales (e.g.,Achnanthes brevipesAgardh). The presence of multiple pathogens in several epipelic diatom taxa suggests a significant role for fungal parasitism in affecting microphytobenthic diatom succession.