Earthen pond rearing system is the most prevalent type of aquaculture facilities in Egypt due to low construction costs. Such facilities are characterized by open nature which allows large numbers of imposing factors to interact with cultured fishes during the production cycle. Aquatic invasive species (i.e., red swamp cray fish: Procambrus clarkii), migratory birds, wild amphibians and reptiles are staggering examples for such interacting factors, which impose severe deleterious impacts on the fish production cycle. The active nature and vast distribution of these species will ultimately violate the rearing regime of the fish farming facility through the establishment, proliferation and spread of pathogens by mechanical, biological and direct infectious routes. Further, the wet nature of aquaculture operations, frequent introduction of new broodstocks, fish meal, reuse of agricultural drainage water and faulty use of animal manure as well as movement of fish from different localities offers a multitude of opportunities for pathogen entry to fish farming operations. Once introduced, pathogens can easily proliferate within the systems leading to potent disease issues, sometimes leading to a complete collapse in production, or more intermittent outbreaks affecting output reliability. Therefore, this study is designated to examine the key role played by invasive species, vectors and reservoirs responsible for pathogen introduction into fish farms. Moreover, the essential needs were discussed for development of practical methods to limit pathogen introduction, spread and proliferation at any level of fish production cycle parallel with the adoption of Good Aquaculture Practice (GAP) and Hazard Analysis and Critical Control Points (HACCP) in Egyptian fish farms.