In the Czech Republic, the Thaya is the seventh longest river in the country with a length of 196.2 km (121.9 mi).

The river flows through or along the following municipalities: Raabs an der Thaya, Ludweis-Aigen, Japons, Drosendorf-Zissersdorf, Vratěnín, Stálky, Uherčice, Podhradí nad Dyjí, Oslnovice, Starý Petřín, Bítov, Chvalatice, Lančov, Vranov nad Dyjí, Horní Břečkov, Hardegg, Lukov, Podmolí, Havraníky, Znojmo, Dobšice, Dyje, Tasovice, Krhovice, Strachotice, Slup, Valtrovice, Křídlůvky, Jaroslavice, Hrádek, Dyjákovice, Laa an der Thaya, Hevlín, Hrabětice, Hrušovany nad Jevišovkou, Wildendürnbach, Jevišovka, Drnholec, Brod nad Dyjí, Dolní Dunajovice, Pasohlávky, Dolní Věstonice, Pavlov, Milovice, Přítluky, Bulhary, Lednice, Podivín, Ladná, Břeclav, Bernhardsthal, Rabensburg, Hohenau an der March and Lanžhot.

Among the protected species that live in the river are the European crayfish and brown trout.

[1] The area of the confluence of the Morava and Thaya, which also includes many pools, oxbow lakes and channels, is the most valuable ichthyological site in the country.

About 209 km (130 mi) of the river is navigable, including almost the entire flow in the Czech Republic.

The river flows through the tourist-attractive areas of the Podyjí and Thayatal national parks, and through the Lednice–Valtice Cultural Landscape, which is included on the UNESCO World Heritage List.