The longest river in Estonia is the Võhandu River (also known as the Voo River, called Pühajõgi in the upper reaches). The Võhandu River is located in Southeast Estonia, with a length of 162 km, a watershed area of 1420 km2, and an average flow rate of 10–11 m3/s.
| River | Length (km) | Watershed (km2) |
|---|---|---|
| Võhandu | 162 | 1420 |
| Pärnu | 144 | 6920 |
| Põltsamaa | 135 | 1310 |
| Pedja | 122 | 2710 |
| Keila | 116 | 682 |
| Kasari | 112 | 3210 |
| Piusa | 109 | 796 |
| Pirita | 105 | 799 |
| Emajõgi | 101 | 9740 |
| Navesti | 100 | 3000 |
| Jägala | 97 | 1573 |
| Vigala | 95 | 1580 |
| Ahja | 95 | 1070 |
| Õhne | 94 | 573 |
| Halliste | 86 | 1900 |
| Valgejõgi | 85 | 453 |
| Mustjõgi | 84 | 1823 |
| Väike Emajõgi | 83 | 1380 |
| Narva | 77 | 814 |
| Reiu | 73 | 917 |