From the geomorphologic point of view, the Neris Regional Park covers a complex and interesting section of the Neris valley. The Neris is a unique river, because, in the territory of Lithuania, practically all the bed is natural except for the segment of several kilometres long in the centre of Vilnius, where the banks of the river are fortified. In 1940, the Neris was tried to dam 2 times, but fortunately, these dams were not built. The Neris valley is deep, 40-50 meters in depth with distinct terraces. The river in the territory of the park makes several turns of different size. The width of the valley in different places is not equal. It is the broadest near Paaliosė – about 4 km wide. 

    The Neris Regional Park encompasses 40 km segment of the Neris midland at the distance of 137-97 km from its mouth. The height of the water fall in this segment is 17 m., the average inclination is 0.42 m/km, the water yield is 119-122 m³/s. The absolute majority of the streams of the Neris Regional Park are still natural. In the territory of the park, the Čekonė, the Saidė, the Vilba, the Bražuolė, the Elna, the Dūkšta, the Aliosė, the Rūgtupis and some more nameless tributaries flow into the Neris. Most of them are short, 1-3 km long, having a great inclination of up to 30-40 m/km, and poorly watery, therefore they episodically run dry.

    In the segment of the territory of the park, there are about 20 sandbars and rifts. The Saidė rift is one of the greatest rifts of the Neris, which is between Volai village and Saidžiai village. It consists of several thresholds; its inclination is 1 m/km. The Neris in this segment crosses the main ridges of the Baltic hills. The depth of the river here is about 1 m, the speed of the torrent is 1.5-1.9 m/s. Here the river does not freeze even during severe frosts.

    In the territory of the Neris Regional Park, there are several lakes; the greatest of them is Velniakampis with the area of 8 ha. A little farther to the south, near Legotiškės, there are 5 non-sloping lakes: Dumbliukas, Ilgelis and three nameless ones. All of them are in thermal karst dips. These lakes are overgrowing; they are surrounded by small wetlands, therefore it is impossible to bathe here. On the left bank of the Neris, in Paaliosė forest, there are 2 Vepriai lakes. They are non-sloping lakes. The green-colour water, showing the accumulated bottom carbonaceous sediments, distinguishes one of them.

    In the deeply cut Neris valley, there are several tens of springs. The most springs are where the riverbed approaches the main slope. The slopes and valleys of the Bražuolė River and the Aliosė River are especially springy.