| Harbor Name | Harbor Notes | Count per Area | Initial Application Date |
| Bellamy River (H) | Scammel Bridge clearance | 1 | 26-Jan-07 |
| Bellamy River (NS) | Scammel Bridge clearance | 0 | |
| Cocheco River (H) | 3 | 30-Sep-04 | |
| Cocheco River (NS) | 3 | 30-Sep-04 | |
| Exeter Town Landing (H) | 6 | 05-Apr-05 | |
| Exeter Town Landing (NS) | 4 | 05-Apr-05 | |
| Gosport Harbor (H) | (Isles of Shoals) | 64 | 26-Feb-88 |
| Gosport Harbor (NS) | (Isles of Shoals) | 5 | 05-Sep-00 |
| Great Bay (H) | 5 | 17-Sep-03 | |
| Great Bay (NS) | 0 | ||
| Hampton (H) | 0 | ||
| Hampton (NS) | 0 | ||
| Hampton: Area 1 (H) | In the vicinity of the boat ramp at Hampton Beach state park | 37 | 21-Aug-90 |
| Hampton: Area 1 (NS) | In the vicinity of the boat ramp at Hampton Beach state park | 9 | 21-Jan-99 |
| Hampton: Area 2 (H) | Extending northwest from Area 1, in the tidal flats up to the area known as the Willows | 40 | 21-Aug-90 |
| Hampton: Area 2 (NS) | Extending northwest from Area 1, in the tidal flats up to the area known as the Willows | 12 | 21-Jan-99 |
| Hampton: Area 3 (H) | In the Hampton River in the vicinity of Blind Creek and Tide Mill Creek, northwest of Area 2 | 20 | 22-Nov-00 |
| Hampton: Area 3 (NS) | In the Hampton River in the vicinity of Blind Creek and Tide Mill Creek, northwest of Area 2 | 5 | 07-Jun-04 |
| Hampton: Area 4 (H) | In the Hampton River, north of Area 3, by Nudds Canal | 19 | 22-Jul-02 |
| Hampton: Area 4 (NS) | In the Hampton River, north of Area 3, by Nudds Canal | 3 | 12-Jul-06 |
| Hampton: Area 5 (H) | North of Great Boars Head on the oceanfront, in the vicinity of North Beach and Plaice Cove | 1 | 29-Jan-07 |
| Hampton: Area 5 (NS) | North of Great Boars Head on the oceanfront, in the vicinity of North Beach and Plaice Cove | 0 | |
| Lamprey River (H) | 6 | 11-Mar-93 | |
| Lamprey River (NS) | 1 | 13-Jan-05 | |
| Little Bay (H) | 0 | ||
| Little Bay (NS) | 0 | ||
| Little Bay: Area 1 (H) | In the vicinity of Upper Fox Point just south of Fox Point | 5 | 20-May-03 |
| Little Bay: Area 1 (NS) | In the vicinity of Upper Fox Point just south of Fox Point | 0 | |
| Little Bay: Area 2 (H) | The Fox Point area, east of Fox Point | 8 | 20-May-03 |
| Little Bay: Area 2 (NS) | The Fox Point area, east of Fox Point | 0 | |
| Little Bay: Area 3 (H) | The Adams Point area, extending about 1/4 mile north of Adams Point | 9 | 27-Feb-04 |
| Little Bay: Area 3 (NS) | The Adams Point area, extending about 1/4 mile north of Adams Point | 0 | |
| Little Bay: Area 4 (H) | The Scammel Bridge area, immediately adjacent to and south of the Scammel Bridge including the area around Cedar Point on the west and extending to Boston Harbor Road to the east. | 17 | 22-Jan-04 |
| Little Bay: Area 4 (NS) | The Scammel Bridge area, immediately adjacent to and south of the Scammel Bridge including the area around Cedar Point on the west and extending to Boston Harbor Road to the east. | 2 | 22-Jan-04 |
| Little Harbour (H) | 176 | 24-Nov-92 | |
| Little Harbour (NS) | 24 | 16-Feb-93 | |
| Newfields Town Landing (H) | 1 | 28-Feb-07 | |
| Newfields Town Landing (NS) | 0 | ||
| Oyster River (H) | 9 | 05-Feb-93 | |
| Oyster River (NS) | 3 | 05-Feb-93 | |
| Piscataqua River (H) | Broken into 6 Areas Below Choose 1 or more | 6 | 23-Feb-98 |
| Bloody Point (H) | Bloody Point Harbor | 14 | 26-Feb-99 |
| Bloody Point (NS) | Bloody Point Near Shore | 0 | |
| Hilton Park (H) | Hilton Park Harbor | 33 | 26-Feb-99 |
| Hilton Park (NS) | Hilton Park Near Shore | 3 | 07-Jun-04 |
| Newington Town Landing (H) | Newington Town Landing/Patterson Lane (H) | 7 | 26-Feb-99 |
| Newington Town Landing (NS) | Newington Town Landing/Patterson Lane (NS) | 0 | |
| Goat Island - Back (H) | 60 | 10-Feb-04 | |
| Goat Island - Back (NS) | 21 | 22-Jul-94 | |
| Goat Island (H) | 92 | 19-Jul-88 | |
| Goat Island (NS) | 8 | 03-Aug-02 | |
| Hart's Cove (H) | 100 | 01-Aug-91 | |
| Hart's Cove (NS) | 6 | 04-Aug-98 | |
| Peirce Island (H) | 91 | 24-Aug-87 | |
| Peirce Island (NS) | 4 | 03-May-01 | |
| Peirce Island Back (H) | 34 | 14-Feb-03 | |
| Peirce Island Back (NS) | 5 | 23-Feb-04 | |
| North Mill Pond (H) | 14 | 07-May-03 | |
| North Mill Pond (NS) | 3 | 19-May-03 | |
| Portsmouth Yacht Club (H) | 109 | 01-Mar-84 | |
| Portsmouth Yacht Club (NS) | 8 | 27-Feb-97 | |
| Rye (H) | 150 | 27-May-86 | |
| Rye (NS) | 25 | 23-Apr-90 | |
| Sagamore Creek (H) | 36 | 24-Apr-90 | |
| Sagamore Creek (NS) | 10 | 03-May-01 | |
| Seabrook (H) | 24 | 21-Jun-05 | |
| Seabrook (NS) | 6 | 08-Mar-06 | |
| TOTAL | 1367 |