(edit) If the airport runway is next to the sea, it would make sense to fly in from the sea to land on the runway towards inland.
That's what the pilot was trying to do, but he misse the start of the runway. (edit)
Why all the talk about altitude readout mismatch and transponders? It was daytime in near perfect visibility with no storms. The pilots can see clearly how high they were in relation to the runway.
Saw the map. The proper name is Ngurah Rai International Airport though TV news casters call it Denpasar Airport. Runway is 8,858 feet or 2,700 m. Changi Airport runway is 4,000m.
A lucky escape.
The water must be shallow there. Or else whole plane under water and all passengers+crew drowned.
If plane had landed a bit to the right, it would have hit rocks, exploded and burnt all passengers+crew.
Oh, the plane was trying to land on the runway in the direction from the sea. The plane did not even manage to land on the runway.
It missed the start of the run way and landed in the water instead. Looks like the pilot aimed wrongly.
Or he had too much blind faith in the instrument landing system (ILS).
Maybe some of the early reports by blur journalists were wrong - that the plane overshot the runway and ended in the sea.