Recent studies have sought to optimize the fecal flotation procedure to improve the detection of helminth eggs in terrestrial domestic species. It is unclear, however, whether these efforts in optimization are applicable to parasite species of marine environments, and verification of veterinary diagnostic procedures is clinically important. It was hypothesized that the eggs belonging to the parasites of pinnipeds would have different specific gravities (SpG) than those belonging to terrestrial hosts. Fecal samples were collected from each of 25 stranded pinnipeds representing three species (Zalophus californianus, Phoca vitulina, Mirounga angustirostris), and modified double centrifugal flotations were performed on 1-g samples. Among the 22 California sea lions sampled, trematode, ascarid, and cestode eggs were detected in 17/22 (77%), 10/22 (45%), and 4/22 (18%) individuals, respectively. Sugar-gradient modified centrifugation flotations were then conducted on a subset of 10 samples from California sea lions to evaluate the distribution of eggs in fractions representing varying SpG. Higher numbers of ascarid eggs were found in fractions representing a lower SpG (1.00–1.15), whereas trematode eggs belonging to the genus Zalophotrema were found in significantly higher numbers in the fraction representing 1.25 (P < 0.05). In conclusion, the SpG of trematode, ascarid, and cestode eggs from pinnipeds appears to be similar to those from terrestrial hosts, but numerous factors may affect their ability to be detected using traditional diagnostic approaches. Further exploration into the nature of the variability noted may lead to improved diagnostics in marine parasitology.