It belongs to the inflow-sinkhole plains. Because of the less permeable Triassic dolomite that traverses the plain, the surface is crossed by streams that flow from the east (Žerovniščica, Šteberščica). A belt of less permeable rocks also occurs at the southeastern edge of the plain, through which underground watercourses that have sunk in Loško polje, and waters from beneath mount Snežnik and Javorniki hills rise to the surface.
The level of the intermittent lake changes with the seasons and the amount of rainfall. At the highest water level the lake is 10.5 km long and 4.5 km wide, and the waters flood up to 29 km² of the field. In this case the lake stretches along the foot of Javorniki along the entire Cerknica Valley, from the villages Gorenje Jezero and Laze in the southeast, to the village of Dolenje vas in the west of the valley, and from the village Otok and the foothill of the Javorniki to the villages Grahovo, Martinjak, Dolenje Jezero in the northern part of the valley.
Water flows into Lake Cerknica from several directions. From the Loška dolina valley it enters through the underground cave system of the swallow hole Velika Golobina, which after almost two kilometres of underground flow emerges at many springs on the eastern edge of Lake Cerknica. The main and largest watercourse of Lake Cerknica is Stržen, which at its source is called Obrh.
In the northern part of the Cerknica plain water emerges at several springs, among which the largest are Šteberški Obrh and Žerovniščica. The only longer surface inflow to Lake Cerknica is Cerknščica, into which waters from the edge of Otave, Vid and Bloke plateaus gather. Under the Slivnica massif there are smaller inflows into the lake: Grahovščica, Martinjščica, the spring of St. Vid and the spring of Mary Magdalene.
On the southern side, beneath the Javorniki hills, there are larger springs: Laški studenec, Tresenec, Retje, Otoški obrh, Mrzlek, Vranja jama in Zadnji kraj, as well as Skadulca and the spring in Ušiva Loka.
At low water levels, the most water disappears through swallow holes Rešeto, Vodonos, Svinjska jama, Mala and Velika Ponikva, Ajnci, Kotel, Jelenšca, Zajcevke, Gebno, Skednenca and Retje, from which it flows toward the sources of the Ljubljanica river in Bistra. At higher water levels, most of the water drains to the northwest, where the water caves Velika and Mala Karlovica remove water toward Rakov Škocjan valley.
