[1] In the upper course, from Võrtsjärv to Kärevere bridge, the river flows through large, flat and marshy areas, which are part of Alam-Pedja Nature Reserve.

In this heavily meandering section, Emajõgi lacks a clearly defined floodplain – the flooded area spans several kilometres at times and has no definite borders.

In the middle course from Kärevere to Kavastu through Tartu, Emajõgi follows a straighter course and flows in a clearly defined, shallow valley mostly a maximum of 10 m (33 ft) deep.

In the past, it has also been an obstacle for land transport between Northern and Southern Estonia, because the river flows in a low-lying and swampy valley.

[2] Due to its location on the crossing of land and water routes, Tartu became an important trading center in Ancient Estonia.

The main type of vessel used was the lodi, a small river barge or sailing ship adjusted for navigation on Lake Peipus and Emajõgi.