Waksmund lies at an elevation of 565 metres primarily on the south bank of the river Dunajec in a hollow between two fossil sandar from the ice age. On the north bank of the Dunajec the land rises abruptly into the Gorce Mountains, on the south bank it slopes much gentler further south until it reaches the foothills of the Tatra Mountains some 6 to 8 kilometres further to the south near Białka Tatrzańska. The westernmost outlier of the Pieniny range, Gisowa Skała, lies a few kilometres to the southeast of the village near to Gronków.