About 300 carp weighing up to 10lbs in a channel close to a lake at IBM, in North Harbour, Portsmouth, have been killed by prymnesium algae, which blocks their gills preventing them taking in oxygen.
A barrier will now be put in place to stop the fish going into the channel . Those that can be saved will be caught, cleaned and returned to the lake. Only 10 per cent were hit by the algae.
The lake is leased by the Portsmouth and District Angling Society which says that although it doesn't own the fish the problem will cost the club around £6,000 to replace them.
Club secretary Dave Coombs said: 'This will have a knock-on effect and will cost us a lot of money. I have already had 20 calls from people to say they were going to join the club early to fish in the IBM lake but now they won't.'
The Environment Agency was called in after the angling society found out about the dead fish on Sunday. After taking samples of the water and running tests it discovered the prymnesium algae, which can kill fish although it is not harmful to humans.
Lucy Harding, a spokeswoman for the agency, said: 'We are looking into ways to help prevent this from happening again. This type of algae is not usually found in this area.'
About a dozen members of the angling society spent nine hours on Sunday in their waders taking the fish out of the water with nets and trying to rescue survivors, which were put into the main lake at North Harbour.
An employee at IBM said: 'It's a really shocking sight, very distressing.
'I would guess that this happened over the weekend, but the fish are still in the water.'