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Hi,
Great choice !
Regarding Azores, I suggest you go to St.Maria.
The marine life and diversity is the best, especially take the Formigas trip and "Baixo do Ambrosio" for special encounters with mobula rays and atlantic goliath grouper. There are several areas around the islands with are protected from fishing, thus allows to see very large specimen.
Please remember must diving in Azores is open ocean with the probability of strong currents and large swell. I experienced 4m waves in the crossing to Formigas. Also important dives are usually quite deep (bellow 25m), usually around wall or underwater peak. Also please bring a surface marker buoy, you will need it.
Weather changing is very fast, there is a local saying "four seasons in one day". In June you can expect good weather, water around 20ºC and good visibility. Watch out for Atlantic bad weather storms, they are becoming more frequent.
For air travel the main airports are in São Miguel and Terceira island, however there is special connection every Thursday direct from Lisbon to Santa Maria (Azores Airlines S4 4012), plus they allow free divers luggage.
For the mainland, there are 3 main areas: near Porto, around Lisbon and on the South "Algarve" zone.
I have just know near South of Lisbon, Sesimbra, mostly the best place to dive in the mainland.
Usually and comparing with Azores water is much cooler (17ºC) and less visibility. Sesimbra is prime location due to South facing position and partial protecting from fishing. You dive all year, weather permitting, and around June the weather is very good with 30-40ºC. Diving is quite shallow (<25m) and good diversity of spots (reef like, wreck and wall).
Regards,
Pedro