AquaMarineDiving Bali
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If you are staying at Villa Markisa (good choice
) then you do not need to stay at Scuba Seraya as they are v close 
Other than that, there's not much for me to add ... yes, you could go up and stay in Pemuteran in NW Bali so you can dive over at Menjangan Island (good wide-angle and macro, good viz, warm water), and can easily get to Secret Bay/Gilimanuk (muck) on the underside of the NW point of Bali, and to Puri Jati (muck) at Seririt on the N coast. Also 'Mimpi Channel' (you don't have to stay at Mimpi Resort to dive there) for Mandarinfish.
To dive outside Padangbai and Candidasa, you can stay in either place
because your chosen dive company will provide transport, but the boats go from Padangbai.
I'm making the assumption you are photographers as you are staying at Villa Markisa.
Assuming you decide to dive outside Padangbai/Candidasa, you can dive the 'Blue Lagoon Area' which will take in The Jetty: Low viz, if diving on a Sat/Sunday - you really must watch out for fishing lines/hooks from the fishermen above! - where you can expect to see frogfish (inc Giant), last time I was there there were five Rhinopias (Eschmeyeri/Paddleflap and Frondosa/Weedy), lots of tiny, tiny cuttlefish, loads of Helmut gurnard, Fingered dragnet, Bentstick pipefish, Dwarf pipehorse, Orangutan crab, Shaggy frogfish, Crocodile snake eel, Napoleon snake eel, Demon stinger, Cockatoo waspfish, Blue ring octopus, baby Mantis shrimp, school of Chevron barracuda, a huge cuttlefish, and more.
Mimpang and Tepekong are next to each other, can have strong currents.
I personally love the little crescent-shaped island of Gili Biaha a bit further north, and right on Bali's most eastern point is Gili Selang.
You mentioned diving at Nusa Lembongan. Most of the dive sites are actually around Nusa Penida (the largest of the three offshore island) including Manta Point I and II, Manta Bay, and that (Nusa Penida) where you are most likely to see Mola-Mola (actually, they're Mola ramsayi, but Mola-Mola has a better ring!) - although you could ask if they've been seen at Mimpang yet as they tend to move to the mainland as the 'season' progresses.
For diving Nusa Lembongan/Penida, you have a choice of staying on the mainland or staying on N Lembongan. If you choose the latter, I'd suggest you dive with either World Diving Lembongan - Home or Scuba diving in Bunaken, Lembeh, and Nusa Lembongan, Bali - Two Fish Divers.
If you would like any further advice (eg: Candidasa accom), please feel free to e-mail me (no sales pitch).
Annabel


Other than that, there's not much for me to add ... yes, you could go up and stay in Pemuteran in NW Bali so you can dive over at Menjangan Island (good wide-angle and macro, good viz, warm water), and can easily get to Secret Bay/Gilimanuk (muck) on the underside of the NW point of Bali, and to Puri Jati (muck) at Seririt on the N coast. Also 'Mimpi Channel' (you don't have to stay at Mimpi Resort to dive there) for Mandarinfish.
To dive outside Padangbai and Candidasa, you can stay in either place

I'm making the assumption you are photographers as you are staying at Villa Markisa.
Assuming you decide to dive outside Padangbai/Candidasa, you can dive the 'Blue Lagoon Area' which will take in The Jetty: Low viz, if diving on a Sat/Sunday - you really must watch out for fishing lines/hooks from the fishermen above! - where you can expect to see frogfish (inc Giant), last time I was there there were five Rhinopias (Eschmeyeri/Paddleflap and Frondosa/Weedy), lots of tiny, tiny cuttlefish, loads of Helmut gurnard, Fingered dragnet, Bentstick pipefish, Dwarf pipehorse, Orangutan crab, Shaggy frogfish, Crocodile snake eel, Napoleon snake eel, Demon stinger, Cockatoo waspfish, Blue ring octopus, baby Mantis shrimp, school of Chevron barracuda, a huge cuttlefish, and more.
Mimpang and Tepekong are next to each other, can have strong currents.
I personally love the little crescent-shaped island of Gili Biaha a bit further north, and right on Bali's most eastern point is Gili Selang.
You mentioned diving at Nusa Lembongan. Most of the dive sites are actually around Nusa Penida (the largest of the three offshore island) including Manta Point I and II, Manta Bay, and that (Nusa Penida) where you are most likely to see Mola-Mola (actually, they're Mola ramsayi, but Mola-Mola has a better ring!) - although you could ask if they've been seen at Mimpang yet as they tend to move to the mainland as the 'season' progresses.
For diving Nusa Lembongan/Penida, you have a choice of staying on the mainland or staying on N Lembongan. If you choose the latter, I'd suggest you dive with either World Diving Lembongan - Home or Scuba diving in Bunaken, Lembeh, and Nusa Lembongan, Bali - Two Fish Divers.
If you would like any further advice (eg: Candidasa accom), please feel free to e-mail me (no sales pitch).
Annabel