Swan Marker David Barber and his team travel up-river in six rowing skiffs
There are fears that the high water levels on the River Thames are stopping swans from breeding successfully.
The concerns were raised by David Barber, the Queen's Swan Marker, as the ancient ritual of swan counting on the river was set to start on Monday.
Mr Barber and his team of Swan Uppers begin their annual task in Sunbury, Surrey, and spend five days rowing through Berkshire towards Oxfordshire.
He said many nests would have been washed away by the strong currents.
Mr Barber said: "Last year saw significantly lower cygnet numbers than usual and it would appear that the situation has not improved in 2008.
"High water levels and strong currents in early June have washed away many nests and young cygnets struggle to survive once separated from their parents."
He said many local schools will be meeting the Swan Markers and Swan Uppers at various locations en route to Abingdon, Oxfordshire, to learn about the birds.
"Regrettably, vandalism remains a major issue affecting mute swans throughout the United Kingdom," Mr Barber added.
The traditional count now serves a conservational purpose
"One of the aims of Swan Upping is to help children to understand and appreciate the problems faced by wildlife in an attempt to avoid vandalism in the future."
Every year a flotilla of Thames rowing skiffs filled with scarlet-coated crews carry out the bird census and each boat flies appropriate flags and pennants.
When a brood of cygnets is sighted, a cry of "All up!" is given to signal that the boats should get into position.
All the unmarked, mute swans and cygnets found are then weighed, ringed and checked for signs of disease or injury.
On passing Windsor Castle, the rowers stand to attention in their boats with oars raised and salute Her Majesty The Queen, Seigneur of the Swans.
The ceremony dates back to the 12th Century when the ownership of all unowned mute swans in Britain was claimed by the Crown in order to ensure a ready supply for banquets and feasts.
Swan Upping now serves a conservational rather than culinary purpose.