How do movies like The Poseidon Adventure (1972) do floods and rogue waves?

For the rogue wave, a scale model was used.

At 1/48 scale the miniature, supervised by Gaile Brown, was 21 feet 6 inches (6.5 m) which was considered a little small at the time, the general rule being that miniature ships should be at least 3/4 inch to the foot or 1/16 scale. After having experience shooting the Tora Tora Tora miniatures at fairly high frame rates L.B. Abbott reasoned he should be able to employ this technique, shooting at seven times normal speed or around 168 frames per second and achieve the desired shots. Another bonus to the smaller scale was that the miniature could also fit in the 32 foot by 14 foot deep (9.75m x 4.2m) Green tank for the underwater shots so only one miniature would be needed. The cost of the miniature to build in 1972 was $35,000 and it ended up weighing around 3 tons.

The capsizing wave was generated by two dump tanks placed in the far right back corner of the tank. The first take had the two towers dumping a full 1200 gallons each which resulted in a massive wave that instantly engulfed the ship obscuring it completely. The miniature was hurriedly repaired ready for the next take where the dump tanks were only half filled. That take had only one of the dump tanks trigger producing an under sized wave so a third and ultimately successful take 3 was called for. Source

For the flooding scenes inside the ship

Quite simply, this was entirely practical. Giant tanks of water (called dump tanks) are used to pour real water quickly causing waves and flooding on the set which was specially constructed to hold water until it was necessary to remove it.

This set was an extremely ingenious piece of work. It was an exact duplicate of its prototype on the Queen Mary in everything but a few details of decor, one of which was a replica of a famous antique statue of the god, Poseidon, except for a slight alteration. The original is equipped with standard genitalia while a design preserves the modesty of the replica. This was not prudishness on the part of producer Allen, but the desire not to distract from important scenes played in front of the figure. So devised was this set that in sections, it could be tilted up to 30 degrees for the beginning of the roll-over sequence. Since it was used in both right-side-up and upside-down sequences, it was designed for speedy conversion: the ceiling being carpeted on its reverse side while the floor had the celling decor on its opposite end. It ultimately was rigged to hold water four feet deep for the sequence in which the sea bursts in to drown the multitude. Source

Most of the scenes are shot using the actual actors

While stunt men had little to do in "doubling" the stars, there were more of these men and women used in The Poseidon Adventure than in any film in recent years, according to Paul Stader, stunt coordinator. Some of this came from stunt people demonstrating to the actors how they should handle hazards and then acting as "backup men" to see that nothing went wrong.The main employment came in such sequences as the one in which 120 persons who had failed to heed Hackman's plea to follow him to safety, are inundated and drowned in thousands of gallons of water. Incidentally, in this connection, it might be noted that The Poseidon Adventure is quite possibly the "wettest" production ever. It is estimated that over 3,500,000 gallons of water was poured into it. Source