The cluster of young swans are believed to have been swimming alone around Thorplands Lake since Monday, after their mother went missing on Sunday.
The male of the family disappeared four weeks ago, leaving the youngsters without a father.
Bodies of neither of the birds have been seen in the area.
Roy Marriott, of rescue charity Animals in Need, said the latest disappearances took the number of swans missing in Northampton to three in recent weeks.
A cygnet disappeared from Delapre Lake two weeks ago.
And Northamptonshire Police said its wildlife liaison officer had reports that fewer swans than usual were living in the Storton's Pits nature reserve at Sixfields.
Mr Marriott said: "I have known the two swans on Thorplands Lake for 14 years and they have become like pets to me.
"For them to leave suddenly, within weeks of each other, would be highly unusual.
"There's no way whatsoever they would leave their young. They just don't do it. I am certain there has been human intervention of some sort."
The RSPCA said it was not aware of any wider problems of stealing swans in Northampton, but a spokeswoman said the organisation would urge any witnesses to report thefts to it or the police.
Glynne Malkin, a police wildlife liaison officer, said: "Although we have not had reports of swans being stolen recently, we have heard anecdotally that there are less swans living in the Sixfields area at the moment than normal."
He added that anyone who witnessed cruelty to swans should contact police on 08453 700700.
Mr Marriott said he would give £100 for information leading to the prosecution of anyone for taking swans in Northampton.
To this day, the Queen of England has prerogative over all swans in England and Wales.
Anyone with information can call 079500 62775.
nick.spoors@northantsnews.co.uk