The Morava originates on the Králický Sněžník mountain in the north-eastern corner of Pardubice Region, near the border between the Czech Republic and Poland and has a vaguely southward trajectory.

[2] The lower part of the river, downstream of the confluence with the Thaya at Hohenau an der March, which today marks the Austro-Slovakian border, is one of the oldest national boundaries still extant in continental Europe: it was the eastern boundary of the Carolingian Empire with the Avar Khaganate around 800, and from the 10th century onward marked the border of the Imperial marcha orientalis, later Duchy of Austria, with the Kingdom of Hungary (within the Habsburg monarchy during 1526–1918 because of imperial expansion).

In July 1997, the Morava basin (especially its northern and eastern part) was affected by heavy stratiform rain, which lasted several days and caused catastrophic floods.

In the Czech Republic, several larger cities and towns lie on the Morava, particularly Olomouc, Kroměříž, Otrokovice, Uherské Hradiště, Veselí nad Moravou and Hodonín.

[2] Downstream of Hodonín, the river flows along a sparsely inhabited, forested border area, all the way to its outfall into the Danube, just below Devín Castle on the outskirts of the Slovak capital Bratislava.

Its weak slope across flat plains furthermore means that the river is prone to meander and flood, creating vast floodplains.

During the 20th century however, large tracts of the river, especially downstream from Litovel, have been regulated with the ensuing effect of loss of inundation areas (floodplains).