Quick answer: April to October, the dry season, for clear water, sunshine and surf. July to October for the best chance of mola mola. Avoid arriving or leaving on Nyepi (Monday 8 March in 2027), when no boats run.
There is no bad month on Lembongan, only different islands. The year splits into two seasons, set by the monsoon winds.
Dry season: April to October
The southeast trade winds blow steadily, skies are mostly clear and the water is at its clearest. The winds blow offshore on Lembongan's northwest reefs, which is why this is surf season. July and August are the busiest months, when Europe and Australia are on holiday, so book boats and beds early.
Sunfish season: roughly July to October
In the cooler months, cold water rises from the deep around Nusa Penida and brings the oceanic sunfish, or mola mola, up to the reef to be cleaned. The peak is usually August and September. Sightings are never guaranteed, but this is the window divers come for. The same cold upwellings can make the water surprisingly chilly; a wetsuit helps. More on the marine life.
Wet season: November to March
Rain usually comes in heavy afternoon or night-time showers rather than all-day grey, and the island turns green. It is quieter and easier to find a room. The sea can be rougher and the water less clear after rain, and some crossings are bumpier.
Nyepi, the Day of Silence
Nyepi is the Balinese new year, usually in March, and it applies on Lembongan too. For 24 hours there are no boats, no flights, no lights, no noise and no going out, including for visitors. The night before, villages parade giant ogoh-ogoh figures through the streets and then burn them. It is one of the most remarkable nights of the year, but you must be on the island before it starts, and you can't leave until it ends. The date moves each year with the Balinese calendar: in 2027 it is Monday 8 March, with the ogoh-ogoh parades on the evening of Sunday 7 March. Boats to the islands also stop for Nyepi Laut, a separate day of silence at sea. Check both before you book.

Ceremonies through the year
Temple festivals happen all year, following the Balinese calendar. If you see a procession on the road, pull over and wait; it's part of island life, not a show.
Questions
What is the best month to visit Nusa Lembongan?
April to October, the dry season, for clear water and surf. May, June and September are a good balance of good weather and fewer people.
When is the rainy season on Nusa Lembongan?
Roughly November to March. Rain usually comes in heavy afternoon or night showers, and the island is greener and quieter.
When can you see mola mola near Nusa Penida?
Mostly in the cooler months, roughly July to October, when cold water rises from the deep. Sightings are never guaranteed and it is mainly a diving encounter.
Can I visit Nusa Lembongan during Nyepi?
Yes, but you must arrive before it starts and stay inside for 24 hours. No boats run in or out on the day.
Where to stay
Snorkelling and mantas
Beaches for swimming