Originally posted by panic_now:

Go to ocean, not just an open water - a region that's called 'Ocean' on minimap. I admit that most times I've seen a serpent was during the night but I can't tell if that's really a boost for chance of encounter or just my personal exp.

...the storms - not sure if they have anything to do with it and probably it was below 1/5 of all times when it was under bad weather

Devs have confirmed that both nighttime and storms boost the serpent chance.

edit: Be wary of fighting them in a really bad storm though. Your ship getting tossed around by the waves can make it hard to land shots on them.