Aquatic fungi were isolated from sea foam, leaf litter, beach sand, and driftwood in an estuary known as "La Boca" (river mouth) of the Manatí River in Barceloneta, northern Puerto Rico. Observations of the baits (sterilized balsa wood) and incubated organic debris, revealed the presence of 28 species of aquatic fungi, 13 of which belong to the ascomycetes and 15 to the mitosporic fungi. The species Arenariomyces triseptatus, Corollospora cf. colossa, C. filiformis, Halosphaeria sp., Kirschsteiniothelia sp., Astrosphaeriella aff. mangrovei, Torpedospora radiata (Ascomycota), Brachiosphaera tropicalis, Campylospora sp., and Clavatospora bulbosa (Mitosporic fungi) were the most common in the samples. Eleven species are new records for Puerto Rico; six fungal isolates could not be identified.