Officers at the Portsmouth & District Angling Society were notified of the problem in the final week of January.
It is estimated that more than 500 fish have died since then, with carp being the species worst affected, alongside some roach and bream.
A mass die-off of this scale has not been seen for more than a decade, according to Steve Mottershead, fisheries officer at the angling society.
He said: ‘It is the most horrible thing I have seen in my life. I cannot explain how horrible it is when you see it. It’s absolutely heart breaking.
‘The first fish was seen about about a week and half ago.’
Now an Environment Agency investigation has been launched to figure out the cause of the environmental crisis.
Steve added: ‘We have taken six fish off to Brampton, which is the head office of the Environment Agency.
‘The local officers have been good – they have given us some likely reasons for it.
‘None of this is concrete, it’s all speculation, but it’s likely there is algae.
Portsmouth & District Angling Society has said the ‘full impact is not known’ and the waters remain shut to anglers.
In a statement on social media, the society said: ‘The water appears to be still suffering and more deaths are likely.
‘We have been working closely with the (Environment Agency) to establish the root cause of the problem, and to this end several surviving fish have been transported alive to the EA labs in Brampton.
‘We have also contacted Portsmouth University experts who are also going to help us assess the fishery. We will await all the findings and any recommendations before we can make any further decisions or plans.
‘This will prevent any further stress being put on surviving fish when they return to feeding. We would like to remind anyone who has fished Lakeside this year to make sure that their fishing equipment is cleaned and dried before using it on any other water.’
The waterways around Lakeside are likely to remain closed for several weeks, according to the society.