David Barber said a number of the birds had died after being injured by dogs while nesting on the River Thames, and there were also reports of egg theft and vandalism.
He was speaking as he prepares to carry out the traditional swan upping ceremony, the annual census of the swan population along the Thames.
Mr Barber said: “We are hoping for an increase in cygnet numbers in 2016 as the total number of cygnets recorded during Swan Upping 2015 was a disappointing 83 compared to 120 in the previous year.
“Once again this year, vandalism has affected many breeding pairs; eggs have been stolen and swans have been attacked by dogs while on their nests in the Caversham, Hurley, Marlow and Maidenhead areas.
“Sadly, some of the injuries sustained by the parent birds have been fatal, resulting in young cygnets struggling to survive on their own against the ever present threats of natural predators. Without the adult birds being present to protect them, many cygnets do not survive such attacks.”
He added: “As part of our aim to promote education and the welfare of mute swans, we ask members of the public to keep their dogs under control when in the vicinity of swans or other wildlife.”
The Swan Upping ceremony dates back to the 12th century when the ownership of all unmarked mute swans was claimed by the Crown in order to ensure a ready supply for feasts.
The Queen’s swan marker counts cygnets each year on stretches of the Thames and its tributaries, and to ensure that the swan population is maintained. This year’s Swan Upping will start on Monday July 18 departing from Sunbury Lock Cut, and will finish at Abingdon Bridge, Oxfordshire on Friday July 22.