When a hatch is opened, water might flow between the two rooms it connects.
This takes no additional time.
If one of the rooms connected by the opened hatch contains a highwater
Flood token and the other room has no Flood token at all, the
water level equalizes between the two rooms: flip the high-water Flood
token to the low-water side, and add a low-water token to the other room.
A player cannot enter a room at high water if he is in a room at low
water (i.e., the room at low water must be pumped before a player may
open the adjoining hatch). Low water never flows into another room,
and water never flows into or out of the sub through an exterior hatch.
If a Flood token is added to a room with a Fire token, the fire is put out:
remove the Fire token. See “Environmental Hazards” on page 13.
When a hatch is opened between a room with a high-water Flood
token and a room with a low-water Flood token or no Flood token
at all, the water level in both rooms becomes low water.
The first set of rules omits anything about high water flow into a low water room, though you could (and probably should) take the ommission as "it doesn't happen" The second rule contradicts that implication by saying that the water will flow.
The first rule says that you can't move through the hatch but then implies you can't open it either, though I don't see how that can be implied when open hatch and stay is a valid choice. If the implied choice is taken then the second rule about high water into low water can never occur in actual play since the hatch will never be opened.