The USS Charon has 13 primary decks and three decks within the sensor pod, however, those decks are normally not inhabited.
Full Deck Listing
Deck 1
Main Bridge, Ready Room, Conference Room, Observation Lounge, Airlock 1
Deck 2
Captain's Dining Room, Captain's Quarters, Executive Officer's Office, Executive Officer's Quarters, Second Officer's Quarters
Deck 3=
Senior Officer Quarters, Junior Officer Quarters, Holodeck 1, Adaptive Recreation Facilities
Deck 4
V.I.P. Quarters, Galley, Officer's Mess, Crew Lounge, Ship's Library, Arboretum (Upper Level), Ship's Chapel
Deck 5
Arboretum (Lower Level), Sickbay, Medical Labs, Counseling Offices, Holodeck 2, Enlisted Crew Mess 1
Deck 7
Chief of Security's Office, Main Brig, Security Offices, Armoury 1, Stellar Cartography, Emergency Transporter 1-5, Auxiliary Control
Deck 8
Enlisted Crew Quarters, Torpedo Storage, Primary Torpedo Bay, Shuttle Control, Shuttle Bay (Upper Level), Workbee Storage,
Deck 9
-Transporter Room 1&2 -Show Pony (Bar & Lounge) -Enlisted Crew Quarters -Shuttle Bay (Catwalk Level) Deck 10
-Shuttle Bay (Lower Level) -Chief of Science Office -Science Laboratories -Aeroponics Lab -Hydroponics Lab -Main Impulse Engines -Antimatter Storage Pods Deck 11
-Antimatter Storage Pods -Enlisted Crew Quarters -Cargo Bays 1 & 2 -Astrogation & Navigational Control -Shuttle Storage -Shuttle Repair Bay -Primary Computer Control -Transporter Rooms 3 & 4 -Navigational Sensor Emitters (Fore and Aft) Deck 12
-Transporter Rooms 5 & 6 -Holodeck 3 -Enlisted Crew Quarters -Upper Core Injection Assembly -Cargo Bays 3 & 4 -Auxiliary Navigational Sensor Emitter (Ventral Exterior) Deck 14
-Enlisted Crew Quarters -Guest Quarters -Engineering (Upper Level) -Cargo Bays 5 & 6 -Enlisted Crew Mess 2 Deck 15
-Engineering (Primary Level) -Chief Engineer's Office -Auxiliary Brig -Auxiliary Security Office -Armoury 2 -Enlisted Crew Quarters -Cargo Bay 7 & 8 -Tractor Beam Emitters Deck 16
-Engineering (Lower Level) -Main Deflector -Deflector Control -Recreation Facilities -Torpedo Storage -Aft Torpedo Bay Deck 17
-Cargo Transporter Pads 1 & 2 -Long Range Sensor Emitter -Industrial Replicators -Storage -Armoury 3 -Airlocks 9 - 12 Deck 18
-Environment Control -Life Support -Cargo Bays 9 & 10 -Gym 1 & 2 Deck 19
- Emergency Transporters 6 - 19 - Springball Court 1 - 3 - Mechanics labs Deck 20
- Sensor Control - Parts Storage - Deuterium Storage - Airlocks 13 - 16