[1][2] The longest tributaries of the Moravian Thaya are:[3] The largest town on the river is Dačice.

The river flows past the municipalities of Panenská Rozsíčka, Bezděkov, Sedlejov, Urbanov, Žatec, Dyjice, Radkov and Černíč in the Vysočina Region, then it continues past Dačice, Cizkrajov, Staré Hobzí and Písečné in the South Bohemian Region before crossing the border into Austria.

From there, the unified Thaya river flows generally eastward and re-enters the Czech Republic.

The river supplies the fishpond Černíčský rybník and a small water reservoir called Ivanka.

[1] About 24 kilometres (15 mi) of the river and its immediate surroundings between Dačice and the Czech-Austrian border are protected as Moravská Dyje Nature Monument.