Wightlink said at 8.16am that it was operating normal services on its Portsmouth Gunwharf to Fishbourne and Lymington to Yarmouth routes, however its FastCat service remained suspended, but would resume at 9.15am.
It said a shuttle service would run from Ryde to Fishbourne to take passengers via the car ferry route.
Hovertravel said at around 8.30am that its services remained suspended.
The Environment Agency issued a flood alert at 10:18am this morning (Monday) for the Eastern Yar and tributaries from Whitwell to Bembridge.
It said: "Following 48mm of rain since 5pm last night (Sunday) the river at Alverstone is continuing to rise and may cause some flooding to low lying areas. The river at Bud Bridge has peaked at 7am today and levels at Alverstone will start falling at around midday."
Isle of Wight Council said at about 11am that the Met Office had lifted its amber weather warning after wind speeds had eased.
*Isle of Wight Airport, Sandown, is closed today and conditions will be assessed before opening tomorrow (Tuesday).