| Abagadasset River | 15 | 15 |
| Alder Stream | 21.3 | 21 |
| Allagash River | 71.8 | 153 |
| Allagash Stream | 23.9 | 24 |
| Androscoggin River | 119.8 | 637 |
| Aroostook River | 106.4 | 392 |
| Austin Stream | 15.2 | 15 |
| Back River | 16.3 | 16 |
| Bartlett Stream | 15.8 | 16 |
| Baskahegan Stream (lower section) | 23.4 | 43 |
| Baskahegan Stream (upper section) | 19.9 | 20 |
| Bear River | 14.6 | 15 |
| Beaver Brook | 9.1 | 34 |
| Beaver Brook - East Branch | 12.1 | 12 |
| Beaver Brook - West Branch | 13.1 | 13 |
| Big Black River | 29.9 | 85 |
| Big Brook | 29.4 | 29 |
| Big Musquash Stream | 5 | 29 |
| Big Musquash Stream - East Branch | 16.1 | 16 |
| Big Musquash Stream - West Branch | 8.2 | 8 |
| Big Wilson Stream | 25.3 | 25 |
| Birch Stream | 27.7 | 28 |
| Black Stream | 17.6 | 18 |
| Bog Brook | 16.3 | 16 |
| Brailey Brook | 22.6 | 23 |
| Captain Ambrose Bear Stream | 16.1 | 16 |
| Carrabassett River | 38.9 | 82 |
| Carrabassett River - West Branch | 12.3 | 12 |
| Cathance River | 17.1 | 31 |
| Caucomgomoc Stream | 19.6 | 37 |
| Chandler River | 24.1 | 24 |
| Charles River | 1.3 | 17 |
| Chemquasabamticook Stream | 31.6 | 32 |
| Chimenticook Stream | 15.6 | 16 |
| Cobbosseecontee Stream | 18.5 | 19 |
| Cold River | 15.5 | 16 |
| Cold Stream | 15.4 | 15 |
| Crooked River (Machias River (Atlantic Ocean tributary)) | 11.7 | 12 |
| Crooked River (Songo River tributary) | 58 | 58 |
| Cupsuptic River | 29.8 | 30 |
| Cuxabexis Stream | 17.3 | 17 |
| Damariscotta River | 18.9 | 19 |
| Dead Brook | 17.5 | 18 |
| Dead Cambridge River | 10.7 | 26 |
| Dead River (Androscoggin River tributary) | 21.3 | 21 |
| Dead River (Kennebec River tributary) | 45.9 | 166 |
| Dead River - North Branch (Kennebec River tributary) | 21 | 21 |
| Dead River - South Branch (Kennebec River tributary) | 26.9 | 27 |
| Dead Stream | 23 | 45 |
| Dead Stream - West Branch | 21.7 | 22 |
| Dennys River | 23.1 | 23 |
| Depot Stream | 30 | 30 |
| Dyer Brook | 15.2 | 15 |
| Dyer River | 20.2 | 20 |
| East Cathance Stream | 13.6 | 14 |
| Eastern River | 14 | 14 |
| East Machias River | 35.8 | 36 |
| Ellis River | 24.6 | 38 |
| Ellis River - West Branch | 13.5 | 14 |
| Falls Brook | 15.3 | 15 |
| Fifteenmile Stream | 17.3 | 17 |
| Fish River | 70.1 | 107 |
| Fish Stream | 25.4 | 25 |
| Fore River | 4.1 | 19 |
| Gilman Stream | 4.2 | 30 |
| Great Works River | 30.3 | 30 |
| Great Works Stream | 22.9 | 23 |
| Greenlaw Stream | 18.8 | 19 |
| Hardscrabble River | 8.2 | 44 |
| Hemlock Stream | 16 | 16 |
| Higgins Stream | 21.1 | 21 |
| Indian River | 16 | 16 |
| Kenduskeag Stream | 41.9 | 42 |
| Kennebago River | 42.5 | 72 |
| Kennebec River | 165.6 | 1,614 |
| Kennebunk River | 17.8 | 18 |
| Kezar River | 14.8 | 15 |
| Kibby Stream | 15.6 | 16 |
| Kingsbury Stream | 19.6 | 20 |
| Lemon Stream | 15.2 | 15 |
| Little Androscoggin River | 53.7 | 70 |
| Little Black River | 29 | 29 |
| Little Machias River | 17.7 | 18 |
| Little Madawaska River | 42.7 | 43 |
| Little Magalloway River | 12.2 | 12 |
| Little Molunkus Stream | 14.7 | 15 |
| Little Ossipee River | 35.9 | 36 |
| Little River (Presumpscot River tributary) | 18.8 | 19 |
| Little River (Salmon Falls River tributary) | 21.3 | 21 |
| Little Spencer Stream | 17.2 | 17 |
| Long Pond Stream | 15.9 | 16 |
| Loon Stream | 17.8 | 18 |
| Machias River (Aroostook River tributary) | 35.5 | 69 |
| Machias River (Atlantic Ocean tributary) | 59.9 | 171 |
| Machias River - South Branch (Aroostook River tributary) | 14.4 | 14 |
| Macwahoc Stream | 25.2 | 25 |
| Magalloway River | 40.1 | 52 |
| Main Stream Sebasticook River | 30.9 | 31 |
| Marsh Stream | 33.5 | 48 |
| Marsh Stream - North Branch | 14.1 | 14 |
| Martin Stream (Kennebec River tributary) | 22.9 | 23 |
| Martin Stream (Nezinscot River tributary) | 15.5 | 16 |
| Martin Stream (Sebasticook River - East Branch tributary) | 23.2 | 23 |
| Mattagodus Stream | 18.2 | 18 |
| Mattakeunk Stream | 16.5 | 32 |
| Mattakeunk Stream - East Branch | 15.7 | 16 |
| Mattamiscontis Stream | 14.7 | 30 |
| Mattawamkeag River | 50.6 | 391 |
| Mattawamkeag River - East Branch | 36.1 | 36 |
| Mattawamkeag River - West Branch | 52.7 | 93 |
| Medomak River | 39.4 | 39 |
| Medunkeunk Stream | 19.4 | 19 |
| Meduxnekeag River | 23.1 | 54 |
| Meduxnekeag River - North Branch | 25.1 | 44 |
| Meduxnekeag River - South Branch | 15.2 | 15 |
| Millinocket Stream | 13.5 | 14 |
| Mollidgewock Brook | 1.4 | 1 |
| Molunkus Stream | 35.6 | 76 |
| Moose River | 83.3 | 98 |
| Mopang Stream | 22.9 | 23 |
| Mousam River | 29.7 | 44 |
| Mousam River - Middle Branch | 13.8 | 14 |
| Munsungan Stream | 17.7 | 18 |
| Musquacook Stream | 20.1 | 20 |
| Narraguagus River | 55.3 | 81 |
| Narraguagus River - West Branch | 25.2 | 25 |
| Nequasset Brook | 17.7 | 18 |
| Nesowadnehunk Stream | 21.9 | 22 |
| New Stream | 15.9 | 41 |
| Nezinscot River | 15.1 | 70 |
| Nezinscot River - East Branch | 19.4 | 19 |
| Nezinscot River - West Branch | 19.8 | 20 |
| Nonesuch River | 25.2 | 25 |
| Northwest River | 16 | 16 |
| Olamon Stream | 22.6 | 23 |
| Old Course Saco River | 21.9 | 54 |
| Old Stream | 24.6 | 25 |
| Orange River | 12.9 | 13 |
| Ossipee River | 13.4 | 13 |
| Oyster River | 13.9 | 14 |
| Passadumkeag River | 48.2 | 48 |
| Passagassawakeag River | 28.4 | 28 |
| Pemaquid River | 23.9 | 24 |
| Penobscot River | 109.4 | 1,818 |
| Penobscot River - East Branch | 74.8 | 204 |
| Penobscot River - North Branch | 26.3 | 26 |
| Penobscot River - South Branch | 38.2 | 38 |
| Penobscot River - West Branch | 116.4 | 301 |
| Pine Stream | 18.5 | 19 |
| Piscataqua River (Atlantic Ocean tributary) | 13.1 | 108 |
| Piscataqua River (Presumpscot River tributary) | 13.2 | 13 |
| Piscataquis River | 65.4 | 386 |
| Piscataquis River - East Branch | 13.9 | 14 |
| Piscataquis River - West Branch | 22.1 | 22 |
| Pleasant River | 14.2 | 14 |
| Pleasant River (Atlantic Ocean tributary) | 44.8 | 56 |
| Pleasant River - East Branch (Piscataquis River tributary) | 32.4 | 44 |
| Pleasant River - Middle Branch (Piscataquis River tributary) | 11.8 | 12 |
| Pleasant River (Piscataquis River tributary) | 15.2 | 95 |
| Pleasant River - West Branch (Piscataquis River tributary) | 35.6 | 36 |
| Pocwock Stream | 18.4 | 18 |
| Presque Isle Stream | 22 | 51 |
| Presque Isle Stream - North Branch | 15.8 | 16 |
| Presque Isle Stream - West Branch | 13.2 | 13 |
| Prestile Stream | 26 | 26 |
| Presumpscot River | 44.7 | 184 |
| Pushaw Stream | 20 | 65 |
| Rapid River | 21.1 | 93 |
| Red River | 15.7 | 16 |
| Roach River | 20.7 | 21 |
| Royal River | 40.5 | 41 |
| Russell Stream | 25.2 | 25 |
| Sabattus River | 16.1 | 16 |
| Saco River | 86.9 | 200 |
| Saint Croix Stream | 20.5 | 21 |
| Saint John River - Northwest Branch | 14.6 | 15 |
| Salmon Falls River | 43.1 | 95 |
| Salmon Stream | 25 | 25 |
| Sam Ayers Stream | 15.5 | 16 |
| Sandy River | 72.3 | 119 |
| Sandy Stream | 26.2 | 26 |
| Sandy Stream - West Branch | 15.1 | 15 |
| Sawtelle Brook | 16.8 | 17 |
| Scarborough River | 3.7 | 29 |
| Schoodic Stream | 16.8 | 17 |
| Scopan Stream | 19.4 | 19 |
| Sebasticook River | 43.5 | 163 |
| Sebasticook River - East Branch | 26.7 | 50 |
| Sebec River | 22.4 | 73 |
| Seboeis River | 28.2 | 45 |
| Seboeis Stream | 9.5 | 41 |
| Seboeis Stream - East Branch | 13.3 | 13 |
| Seboeis Stream - West Branch | 18.1 | 18 |
| Sevenmile Stream | 15.2 | 15 |
| Sheepscot River | 67.8 | 113 |
| Sheepscot River - West Branch | 24.9 | 25 |
| Shepards River | 10.3 | 10 |
| Ship Pond Stream | 9.7 | 26 |
| Skagrock Brook | 16.6 | 17 |
| Songo River | 19 | 77 |
| Souadabscook Stream | 20.9 | 21 |
| South Brook | 19.3 | 19 |
| Spencer Stream | 24 | 57 |
| St. Croix River | 74.7 | 141 |
| St. Francis River | 40.6 | 73 |
| St. George River | 55.6 | 85 |
| Stillwater River | 11.4 | 104 |
| St. John River | 162 | 1,249 |
| St. John River - Baker Branch | 49.3 | 88 |
| St. John River - Little Southwest Branch | 30.9 | 31 |
| St. John River - Southwest Branch | 63.4 | 183 |
| Stratton Brook | 15 | 15 |
| Stroudwater River | 15.3 | 15 |
| Sunday River | 14.1 | 14 |
| Sunkhaze Stream | 27 | 27 |
| Swift Cambridge River | 15.3 | 15 |
| Swift River | 27.2 | 27 |
| Temple Stream | 15.2 | 15 |
| Tomah Stream | 37 | 37 |
| Trout Brook | 11.9 | 23 |
| Trout Brook - South Branch | 11.4 | 11 |
| Tunk Stream | 20.1 | 20 |
| Turner Brook | 16.3 | 16 |
| Twomile Brook | 3.8 | 25 |
| Twomile Brook - North Branch | 11.8 | 12 |
| Twomile Brook - South Branch | 9.8 | 10 |
| Union River | 21.8 | 77 |
| Union River - East Branch | 21.6 | 35 |
| Union River - Middle Branch | 13.8 | 14 |
| Union River - West Branch | 20.1 | 20 |
| Violette Stream | 16.3 | 16 |
| Wallagrass Stream | 21 | 21 |
| Wassataquoik Stream | 27.9 | 28 |
| Webb River | 22 | 22 |
| Webster Brook | 9.4 | 33 |
| Wesserunsett Stream | 15.6 | 29 |
| Wesserunsett Stream - East Branch | 13 | 13 |
| Western Little River | 11.2 | 11 |
| Wild River | 4.9 | 5 |
| Wilson Stream | 16.5 | 17 |
| Wytopitlock Stream | 25.5 | 26 |
