Morag Winston left 11-year-old Harry's wheelchair outside their home in Eastgate, Deeping St James, ready for the school bus on Monday just before 8am.
But as the family were eating breakfast, a teenager stole the youngster's bag and coat from the wheelchair before driving off in a car.
A friend of the family later found the bag, which contained important information about his disability, in the River Welland while dog walking in Glinton.
Harry, who has Down's syndrome, autism and a form of epilepsy, attends the Willoughby School in Bourne.
His 45-year-old mum, who is married to Paul and has younger son, Edward, 10, said: "I just feel sad that somebody had actually done it.
"It was obviously a child's wheelchair and to actually do it to a child who has got special needs is even worse.
"You expect things like this to happen in London or a big city but not Deeping St James."
Mrs Winston often leaves Harry's wheelchair outside the family's home ready for the bus to pick up the youngster, who can only walk short distances, but is now going to change the routine.
On Monday the family spotted a boy, aged between 17 and 19, climbing into a dark grey car with Harry's coat and drive off in the direction of Market Deeping.
When Mrs Winston went to the check the wheelchair, she found the schoolbag was missing.
Harry's coat was found up the road by a bus driver.
This bag contained medical equipment, a recording device, clothes and his communications passport, which has information about Harry's disability.
Nothing was taken but Mrs Winston says she will have to replace the recording device, worth £150, as it is now broken and the communications passport because it is water damaged. She creates the passport herself by typing out all his medical information which she says will take her hours.
She said: "They just don't realise what damage they have done when you haven't got the time in the first place to do it and now I'll have to do the passport again."
Anyone with any information can call Stamford Police Station on 01780 752222, quoting incident number 61 of September 15.