Eye flukes in fish are common in freshwater lakes. Fish become infected by the penetration of cercariae released from freshwater snails, and high infection pressures may be associated with mortalities in a Danish lake. Examination of two other freshwater lakes, combined with laboratory study, supported the notion. We investigated 77 freshwater fish from two lakes and the infection level suggested the occurrence of a high cercarial infection pressure in the Danish lakes. Dominant genera were Tylodelphys and Diplostomum covering a range of species identified by PCR and sequencing of the 18S (partial)-ITS1-5.8S-ITS2-28S (partial) of the rDNA. Cercariae of the prevalent species Diplostomum pseudospathaceum were used to infect zebrafish Danio rerio for the elucidation of short-term effects on the fish host. Zebrafish did not display abnormal behaviour when exposed to 200–400 cercariae, but a dosage of 600 and 1,000 cercariae/fish proved lethal. When fish were exposed to sublethal dosages, 19 out of 27 immune genes were significantly regulated and three genes encoding cytokine (IL 4/13B, IL-6 and IL-8) were upregulated at 3 hr post-infection (hpi), whereas others were downregulated especially at a later time point. We suggest that direct massive cercarial penetration of fish surfaces may be detrimental and may represent a threat to fish populations.