Introduction: Endophytic fungi are good sources of bioactive compounds that are exclusive to their hosts. Eichhornia crassipes plant produces different bioactive compounds. The aim of the present study is to isolate and identify endophytic fungi that reside in Eichhornia crassipes tissues, and to evaluate the biological activities of their extracts. Materials and Methods: Endophytic fungal spp. were isolated from leaves and petioles of Eichhornia crassipes, identified and then extracted. The ethyl acetate extracts were tested against bacteria, fungi, hepatitis B virus and Schistosoma mansoni cercariae. The chemical composition of these extracts was determined by Gas chromatography-mass spectrometry (GC-MS/MS) analysis. Results: We found that four fungal spp. were dominant in Eichhornia crassipes; they were molecularly identified as Aspergillus flavus OM758315, Aspergillus fumigatus OM688980, Aspergillus welwitschiae OM758326 and Corynascus sepedonium OM688206, with A. flavus as the most frequent. The ethyl acetate extract of the four fungal spp. showed pronounced antimicrobial effects, whereas the highest antiviral effect on hepatitis B virus was that of A. flavus followed by A. fumigatus extracts. All the tested extracts were cercaricidal to Schistosoma mansoni cercariae, where A. flavus was the most effective. GC-MS/MS analysis indicated the presence of various bioactive compounds. Conclusions: Aspergillus flavus, Aspergillus fumigatus, Aspergillus welwitschiae and Corynascus sepedonium as endophytes of Eichhornia crassipes showed promising antimicrobial, antiviral and cercaricidal properties.