The course of Emajõgi is divided into 3 distinct sections. 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 deep. The width of the valley in the middle course is 1–1.5 km; in Tartu, it narrows to 800 m. The narrowest section of the valley (400–600 m) is located in the end of the middle course near Kavastu. In the lower course, the river flows through a swampy lowland – Emajõe Suursoo – before emptying into Lake Peipsi at Praaga.