ID SciFi series from mid 60's.

I have very vague memories of this one. The heroes were in a base under water and the space ships took off from there. I remember the ships being spinning discs, flying saucer type.
It might be UK made. Or even German.

The British series UFO, syndicated worldwide.

The series was first broadcast in 1970. The secret military defense organization named SHADO has a base on the moon, and a fleet of submarines. Fighter planes are launched from the submarine fleet to fight the invading UFOs.

Perhaps you are thinking of Raumpatrouille - Die phantastischen Abenteuer des Raumschiffes Orion (Space Patrol - The Phantastic Adventures of the Spaceship Orion) from 1966.

Here are some pictures including the underwater base:

This fansite has the Orion starting from the sea as its logo:

Here is a review for all those who have never seen it:

Kellner found it. Thanks.