| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Adma River | River (basin) | native | 89719 |
| Bagmati | River (basin) | native | 9496 |
| Bhimtal Lake | Lake | native | 89721 |
| Cauvery | River (basin) | native | 43636 |
| Chilika Lake/Lagoon | Lagoon | native | 29108 |
| Choto Jamuna | River (basin) | native | 100698 |
| Da River | River (basin) | introduced | 89724 |
| Ethiopian | Zoogeographic realm | introduced | 1739 |
| Gaylegphug | River (basin) | introduced | 40882 |
| Godavari | River (basin) | native | 43636 |
| Jayanti River | River (basin) | native | 89719 |
| Kosi | River (basin) | native | 9496 |
| Krishna River | River (basin) | native | 43636 |
| Laguna de Bay | Lake | introduced | |
| Mekong | River (basin) | introduced | 30857 |
| Nainital Lake | Lake | native | 89721 |
| Naukuchiatal Lake | Lake | native | 89721 |
| Oriental | Zoogeographic realm | endemic | 12076 |
| Palearctic | Zoogeographic realm | introduced | 1739 |
| Periyar | Lake | introduced | 45208 |
| Taal Lake | Lake | introduced | 13446 |