Blue-green algae found in Lough Erne near Castle Archdale
Blue-green algae has been found in lower Lough Erne and the algal bloom on Lough Neagh has moved south, according to council staff in both locations.
The areas affected by the potentially toxic bacteria are the vicinity of Castle Archdale in County Fermanagh and Oxford Island, off Lough Neagh.
Warning signs have been erected.
One family of holidaymakers told BBC News NI they became ill after waterskiing near Castle Archdale last week.
Donna Laughlin from Antrim said her husband and his cousin began to feel unwell a day after they spent time in the water in Lough Erne.
She said her husband had a kidney infection while his cousin "ended up with a really bad sinus and ear infection".
It is not known if the family's problems were linked to blue-green algae but it is known that this particular bacteria can cause illness in humans and is particularly dangerous for exposed pets.
Ms Laughlin said her family did see algae in the water while they were waterskiing, but they did not realise the danger.
"It wasn't apparent at the time - we didn't know the risk factors, obviously. But we soon learned about them afterwards," she said.
Ms Laughlin added that her grandchildren will not be swimming in the lough for the rest of their holiday.
In a post on its website, Fermanagh and Omagh District Council said the Northern Ireland Environment Agency had confirmed the presence of the potentially toxic bacteria "in the vicinity of Castle Archdale".
Armagh City, Banbridge and Craigavon Council said wind direction had pushed the bloom on Lough Neagh south and it had moved from Bartin's Bay to Oxford Island.
"This will continue until there is a change in wind direction or weather change, which will disperse the bloom," it added.
It advised people to avoid contact with the algae and to keep pets and animals out of the water.
Concerns had also been raised along the shore of Lough Neagh in the Washingbay area after a gas-like odour was reported.
It is thought to have been emitted by decaying algal blooms.
Mid Ulster councillor Malachy Quinn said the smell was so strong that he checked his own gas appliances for a possible leak.
He said he received more than 30 messages and calls from concerned constituents, all complaining of the same issue, from the Derrylaughan, Derrytresk, Ardboe and Ballinderry areas.
"They could all smell a very thick smell of gas. To me, it was almost like my gas pipe was leaking or was coming from a gas cylinder - that's how strong it was," the SDLP representative told BBC News NI.
Mid Ulster District Council said that after consulting the fire service, it had "no current concerns regarding gas".
"Very quickly they were able to tell us this was natural," Mr Quinn said. "It was coming off the waterways."
On Thursday, dog walkers at lower Lough Erne changed their plans.
Alanna McCauley brought Riley for a paddle but it was a walk on dry land for them both.
"We'd brought him [Riley] down for a wee dip but I don't think we'll do that now - we'll just try and keep him out of the water."
Ilona Aborneviene with her daughter Karolina Abornevaite decided their dogs would have a forest walk instead of their usual swim.
"The dogs love the water - but because of the algae we're taking the forest route - their safety comes first" said Karolina.
Algal blooms have caused bathing bans along parts of the north coast this summer.
That followed the algae appearing in Lough Neagh in levels not seen since the 1970s.
Algal blooms can produce toxins and remove oxygen from the water as they decompose.