ID SciFi series from mid 60's.

Cafe Society
1

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.

2

The British series UFO, syndicated worldwide.

3

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.

4

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:
http://www.geocities.com/CapitolHill/3589/raumpatrouille.html

This fansite has the Orion starting from the sea as its logo:
http://www.orionspace.de/ww/de/pub/english.htm

Here is a review for all those who have never seen it:
http://www.popcultmag.com/oddglimpses/international/orion/orionlog.html

5

Kellner found it. Thanks.