The Lincoln Swan Project is run jointly by Dr Laetitia Marechal from the University of Lincoln and Dr Jenny Dunne from Keele University. They track the behaviour of more than 300 swans and the public share their sightings on an app.
Marechal said the pair of swans that died were “iconic” in the Brayford Pool area.
“They were there for nearly 10 years and unfortunately they died from avian flu in December, as well as one of the cygnets.
“This strain is called the H5N1 and is highly infectious, so this is linked, unfortunately to a lot of high mortality in birds, in swans, geese and other birds.
Marechal said there is no treatment for affected birds and moving sick birds increases the risk of transmission.
Experts have asked the public to avoid interacting with wild birds and not feed or handle them.
A spokesperson for the Animal and Plant Health Agency said: “We are aware of a number of wild birds deaths in the Lincoln area and two mute swans collected from the Brayford Pool area in November were found positive for highly pathogenic avian influenza.”