| Ecosystem | Type | Status | Ref. |
|---|---|---|---|
| Adma River | River (basin) | native | 89719 |
| Australian | Zoogeographic realm | introduced | 2847 |
| Bensbach River | River (basin) | introduced | 50786 |
| Buhi | Lake | introduced | 13446 |
| Buluan | Lake | introduced | 13492 |
| Buxa River | River (basin) | native | 89719 |
| Chao Phraya River | River (basin) | native | 26336 |
| Chilika Lake/Lagoon | Lagoon | native | 29108 |
| Choto Jamuna | River (basin) | native | 100698 |
| Da River | River (basin) | native | 89724 |
| Great Lake | Lake | native | 36651 |
| Jayanti River | River (basin) | native | 89719 |
| Laguna de Bay | Lake | introduced | 13460 |
| Lake Lanao | Lake | introduced | 10888 |
| Lake Mainit | Lake | introduced | 50320 |
| Mackenzie | River (basin) | native | 4833 |
| Manguao | Lake | introduced | 13489 |
| Mekong | River (basin) | native | 27732 |
| Naujan Lake | Lake | introduced | 13446 |
| Oriental | Zoogeographic realm | endemic | 4833 |
| Poso | Lake | introduced | 26747 |
| Taal Lake | Lake | introduced | 13446 |
| Toba | Lake | introduced | 57970 |
| Tonle Sap | Lake | native | 36651 |