This is an incomplete list of rivers that are at least partially in Malaysia. The rivers are grouped by strait or sea. The rivers flowing into the sea are sorted along the coast. Rivers flowing into other rivers are listed by the rivers they flow into. The rivers that have their mouths in Malaysia are given in italics. The same river may be found in more than one state as many rivers cross state borders.
| International border | River | Area (km2) |
|---|---|---|
| Kelantan–Thailand | Golok River | 1,011.125 |
| Sabah–Indonesia | Sibuku River | 799.452 |
| Sabah–Indonesia | Sembakung River | 5,467.765 |
| Sarawak–Brunei | Pandaruan River | 222.378 |
| State border | River | Area (km2) |
|---|---|---|
| Perlis–Kedah | Perlis River | 724.398 |
| Penang–Kedah | Perai River | 447.824 |
| Penang–Kedah | Jawi River | 231.031 |
| Penang–Kedah–Perak | Kerian River | 1,420.233 |
| Kedah–Penang | Muda River | 4,150.397 |
| Perak–Selangor | Bernam River | 2,836.333 |
| Selangor–Federal Territory | Klang River | 1,297.382 |
| Selangor–Federal Territory | Buloh River | 451.926 |
| Selangor–Federal Territory–Negeri Sembilan | Langat River | 2,347.882 |
| Selangor–Negeri Sembilan | Sepang River | 101.932 |
| Negeri Sembilan–Malacca | Linggi River | 1,297.668 |
| Negeri Sembilan–Malacca | Malacca River | 614.575 |
| Malacca–Johor–Negeri Sembilan | Kesang River | 658.263 |
| Johor–Negeri Sembilan | Muar River | 6,137.800 |
| Johor–Pahang | Endau River | 4,739.059 |
| Pahang–Negeri Sembilan | Pahang River | 28,682.247 |
