Many humic lakes in Northern Europe are dominated in summer by the freshwater raphidophyte Gonyostomum semen. To identify potential interactions with other planktonic organisms, such as predators or parasites, we performed amplicon sequencing of the eukaryotic plankton community in 4 humic lakes over the course of the summer bloom. The surface water samples were size-fractionated to identify small (<10um) parasitic zoospores that were associated with larger host organisms.