Geologically the two islands of Bali and Java were joined until the end of the last ice age when the sea rose and cut the land bridge.

The temperature of the water in Bali Strait is subject to noticeable seasonal fluctuations, predetermined by the periods of monsoons.

Sea currents in the strait have a very complex configuration, largely dependent on monsoon seasons: during the northwesterly winds, the northern vector predominates, while in the south-east it is the southern one.

At the beginning of the 21st century, there were noticeable negative trends in the development of the ecological situation in the strait and on its shores, related to human economic activity.

Numerous cases of water pollution with industrial wastes, fertilizers, as well as chemicals used in gold mining on the Javanese shore are recorded.