Water frogs of the genus Pelophylax host a variety of parasites, from protozoa to helminths. Among the blood parasites, representatives of Apicomplexa, Trypanosoma and Nematoda show the highest prevalence. In this study, we focused on blood parasites of water frogs living in the Danube Delta, Romania. In total, 74 individuals of P. ridibundus and eight individuals of P. esculentus from six localities were examined. Blood parasites were detected microscopically and using a molecular marker (18S rDNA). 89.77% of frogs from all investigated localities were found to be infected with at least one parasitic group, specifically with haemogregarines (84.09%), nematodes (1.14%), and trypanosomes (63.64%). The parasitemia of haemogregarines and trypanosomes differed significantly among the studied locations. There was no statistically significant difference in parasitemia between male and female hosts. However, adults were found to have a significantly higher parasitemia in comparison with subadults infected with haemogregarines. Correlation between parasitemia and the body length of frogs infected with haemogregarines was also significant (r = 0.226). By comparing the 18S rDNA sequences with the corresponding GenBank sequences, Hepatozoon species identified in water frogs showed a close similarity (98.1–99.8%) to Hepatozoon magna. Trypanosomes showed the highest sequence similarity to Trypanosoma sp. isolate R10 clone L2–3, Trypanosoma ranarum, and Trypanosoma cobitis.