Give a stream of consciousness and then the final answer. Filming began with the animals on September 9, 2015, and principal photography with the actors began on September 29, 2015, in Prague, Czech Republic. Suzie Davies served as the production designer, Andrij Parekh as the director of photography, and Bina Daigeler as the costume designer. Filming ended on November 29, 2015.

Answer this question: where did they film the zookeeper's wife?
This is the relevant information: Filming began with the animals on September 9, 2015, and principal photography with the actors began on September 29, 2015, in Prague, Czech Republic.
So, the final answer is Prague , Czech Republic.