| Segment | Name | Salinity Regime |
| CB1 | Northern Chesapeake Bay | Tidal Fresh |
| CB2 | Upper Chesapeake Bay | Oligohaline |
| CB3 | Upper Central Chesapeake Bay | Mesohaline |
| CB4 | Middle Central Chesapeake Bay | Mesohaline |
| CB5 | Lower Central Chesapeake Bay | Mesohaline |
| CB6 | Western Lower Chesapeake Bay | Polyhaline |
| CB7 | Eastern Lower Chesapeake Bay | Polyhaline |
| CB8 | Mouth of the Chesapeake Bay | Polyhaline |
| WT1 | Bush River | Oligohaline |
| WT2 | Gunpowder River | Oligohaline |
| WT3 | Middle River | Oligohaline |
| WT4 | Back River | Oligohaline |
| WT5 | Patapsco River | Mesohaline |
| WT6 | Magothy River | Mesohaline |
| WT7 | Severn River | Mesohaline |
| WT8 | South, Rhode & West Rivers | Mesohaline |
| TF1 | Upper Patuxent River | Oligohaline |
| RET1 | Middle Patuxent River | Mesohaline |
| LE1 | Lower Patuxent River | Mesohaline |
| TF2 | Upper Potomac River | Tidal Fresh |
| RET2 | Middle Potomac River | Oligohaline |
| LE2 | Lower Potomac River | Mesohaline |
| TF3 | Upper Rappahannock River | Oligohaline |
| RET3 | Middle Rappahannock River | Mesohaline |
| LE3 | Lower Rappahannock River | Mesohaline |
| TF4 | Upper York River | Oligohaline |
| RET4 | Middle York River | Mesohaline |
| LE4 | Lower York River | Polyhaline |
| WE4 | Mobjack Bay | Polyhaline |
| TF5 | Upper James River | Tidal Fresh |
| RET5 | Middle James River | Oligohaline |
| LE5 | Lower James River | Mesohaline |
| ET1 | Northeast River | Oligohaline |
| ET2 | Elk & Bohemia Rivers | Oligohaline |
| ET3 | Sassafras River | Oligohaline |
| ET4 | Chester River | Mesohaline |
| ET5 | Choptank River | Mesohaline |
| ET6 | Nanticoke River | Mesohaline |
| ET7 | Wicomico River | Mesohaline |
| ET8 | Manokin River | Mesohaline |
| ET9 | Big Annemessex River | Mesohaline |
| ET10 | Pocomoke River | Mesohaline |
| EE1 | Eastern Bay | Mesohaline |
| EE2 | Lower Choptank River | Mesohaline |
| EE3 | Tangier Sound | Mesohaline |