After the annexation of Austria to Nazi Germany, the authorities expelled the Jewish population from the border region of Burgenland. Some of them were stranded in the no-man's land between Czechoslovakia, Hungary and Austria; none of the countries would let them enter their territory. Schmolkova became involved in their rescue, personally visiting the boat on the Danube where the desperate people were located. Similarly, she helped when Germany deported nearly twenty thousand Jews of Polish origin to Poland, which was unwilling to accept them. But the most difficult situation awaited her at home.
After the occupation of the borderlands in the autumn of 1938, the situation of the refugees in Czechoslovakia turned into a complete disaster. Marie Schmolková did not visit the places where the refugees were gathered, she collected facts that could be used to mobilize public opinion in possible countries of immigration, and she wrote appeals to diplomats of these countries working in Prague and to Jewish organizations abroad. If she could not be found in the office of the Refugee Committee in Jáchymova Street, she worked from here, from home.
Writer and critic Max Brod recalls how he has visited Schmolková on Kamzíková Street countless times to intercede for refugees in distress, shocking cases that needed immediate help. "Every time I dialed her phone number, I felt that help was already close at hand. But everyone called her, and so nine out of ten calls went unanswered. Either she wasn't home or it was busy."
The reporter Milena Jesenská only got to know Marie Schmolkova during the Munich crisis. "She lives in the Old Town in a small alley that I, a native Pragueite, did not know, in a small, crooked house with wooden stairs. But when you enter the apartment, you find a strangely graceful and cultured apartment, beautiful books, Sturs sculptures, beautiful, dark furniture, and a telephone that won't stop ringing."