The river Bodrog is the natural village boundary of Bodrogkeresztúr. Flowing past the Tokaj Mountain, the Bodrog meets river Tisza 3 kilometers away from the municipality. The flood plain of the backwater area between the two rivers is a naturally protected area called Bodrogzug.
The mountain range between Tokaj and Eperjes is part of the inner volcanic belt of the Carpathian Mountains, which was active about 15 million years ago. The Hungarian section of this range is called the Zemplén Mountains.