Marine mammals are known to harbor Cryptosporidium spp. and Giardia spp., especially species or genotypes commonly associated with humans. In animals of the North and Baltic Seas, this information is missing. In this study, fecal samples (n = 97) from harbor porpoises (Phocoena phocoena), harbor seals (Phoca vitulina), and grey seals (Halichoerus grypus) present in German waters were examined via microscopic examination (by using a modified Ziehl-Neelsen technique [MZN]) to estimate the prevalence of these parasites. Additionally, intestinal tissue samples (n = 1,049) from specimens of 10 marine mammal species were submitted for histopathologic examination (HP). A low prevalence was detected (2.1 and 1.3%, for MZN and HP, respectively), associated with Cryptosporidium spp. Giardia spp. was not observed. Current results suggest a low prevalence of these parasites in marine mammals present in Germany. However, methods with higher sensitivity, such as molecular methods, are crucial to confirm the prevalence, establish origin routes, and determine epidemiologic factors associated with the low prevalence observed.