Croatia

The Pazincica River, which flows through the Istrian capital Pazan, ends its course in the Fojba Cave, also known as the Pazinska Cave, 120 m deep.

An excerpt from the article 51 facts about Croatia
Further on, it flows about 100 m below the city, forming two underground lakes connected by a siphon. During heavy rains, the siphon cannot hold all the incoming water, in which case a lake up to 2 km long forms in the Fojba Cave. The lake forms extremely rarely; it was observed in 1883, 1896, 1930, 1935, 1961, 1964, 1974, 1993, and most recently in 2002.