Lt Stephanie Juniper said the Cadets, who meet twice a week and most weekends, could spend up to half an hour of their two-hour sessions removing water from the unit.
She said, "It has gradually been getting worse over five years. Last winter was spent emptying binfuls of water.
"Often I tell people we are the only unit with indoor boating, it gets so wet in here."
The water has infiltrated 10 rooms of the 40-year-old building in Fisherman's Green, ruining uniforms and projects and on one evening almost causing the group to shut down because of concerns about it reaching the electric lights.
The roof will cost £68,000 to fix but, thanks to grants from the government's Youth Opportunity Fund, the Marine Society and the Sea Cadets, only £30,000 remains to be raised.
The unit, which next year celebrates its centenary, unlike the Army Cadets and Air Cadets, is not completely financed by the Ministry of Defence but only receives some funding for training.
Lt Juniper said, "We are always the poor relation even though we are the senior service, which is why we always march in front in parades."
The land its unit is on is owned by Eastbourne Borough Council, to which it pays rent, but any problems with the fabric of the building is the Sea Cadets' to pay for, which is why the group is asking for donations.
Eastbourne Sea Cadets and Marine Cadets is for 10 to 18-year-olds and activities based on the Royal Navy tradition include drills, shooting, cooking, music, first aid and camping. Members can complete their Duke of Edinburgh awards, BTEC qualifications and Royal Yachting Association-approved qualifications in seamanship, sailing, power boating and canoeing, as well as taking part in parades.
To donate money towards the roof repair, become a volunteer for the Cadets or find out more call Lt Juniper on 07725 246470.
victoria.allen@trbeckett.co.uk