You really need to define and formulate your question better. As it stands, it' s quite unclear. Fish farming is a global industry, carried out in variety of open and closed systems, in freshwater, brackish and marine environments. Sometimes, the aquacultured fish may be spreading diseases (e.g. parasites) to wild fish, sometimes, it's the other way around. the question of zoonoses is also a species-specific one. So please tell us more specifically what you want to know.
I did my PhD on that question. It is not as simple an answer as you would expect- because most people think it is due to lack of education, and it is not.
There are several bio-security measures including frequent monitoring of aquaculture facilities, treatment of the pond water with disinfectants, quarantine measures to eliminate the chance of introduction of any unwanted species in the pond and eradicate/treating the the diseased specimens, maintenance of these records, etc. Sometimes farmers refuse to apply bio-security measures either because the farmers are unaware of its impact or sometimes these are expensive to implement. Further, it all depends on the fish species grown, location of the culture pond, awareness/skill of the personnel, business strategies etc.
Biosecurity is also needed for developing and maintaining new hybrid or cultured varieties, for collecting seeds (eggs & sperms) from such genetically modified mature fishes (even prawns), even see weeds.......In fact biotechnological procedures are generally carried out in bio secure areas
Bio security in fish farm we can do that by preventing the pathogens by maintaining the farm condition in a healthy manner by reducing the food wastage which is the major cause for the out break of the pathogens, making favorable environment for the nourishment. We can Prevent most of the pathogens in earlier stages with Probiotics Either through feed or through water . But at latter stages where we have a severe loss and unable to overcome the Disease, No other remedy like going for antibiotics but it effects the growth and also the farm Condition habitat which may take time to recover(Minimum 2 Months). Better to prevent them by giving regular Probiotics and regularly checking the water parameters.
Although biosecurity issues in fish farming is less critical than in the case of poultry set-ups, simple cautions on avoiding introduction of non-native species, proper sanitation of the farms and monitoring water quality should be sufficient.
You might like to read Palić, et al (2015). A Standardized Approach for Meeting National and International Aquaculture Biosecurity Requirements for Preventing, Controlling, and Eradicating Infectious Diseases. J. Appl. Aquacult., 27 (4):185–219.
If funding was available to cover travel and other expenses for the IAVBC team to run a 4-day, hands-on aquaculture biosecurity workshop, we could certainly do this in any country - as we have already done in Norway, Chile, the Cezch Republic, S. Africa and elsewhere. We would need 6-8+ months to prepare, plan and put togeher site- and species-specific workshop manuals for participants.