Monsters will not pursue you across deep water if they do not fly, do not blink (i.e. dar blademasters, imps) and are not aquatic (e.g. nagas). This won't help you against ranged monsters and spellcasters, either.
You can stand in deep water just off a corner and exploit the fact that only one melee monster will be able to reach you to kill them one by one. Or, if you have useful staves, fire them at monsters from the safety of deep water. Or use those darts you've been carrying around all game!
After running across deep water, the monster will only be able to track you by fresh scent. As a result, if you leave no route of scent that takes them from that coastline to your coastline, they won't know how to follow. Once you get out of LOS and wait they will eventually reset to a 'wandering' state and you will be able to escape the level without them pursuing.
As early as depth 2, water is a candidate for containing eels. Eels hit as hard as two jackals at once and are difficult to kill (since they flee after biting you, submerge in deep water and 'flit' making them unpredictable to aim at). The location of eels can be revealed by diving as well, but submerged monsters are almost impossible to target with ranged effects. If you are low on hp and low level, stay away from even shallow water so eels can't bite you to death, and beware the key puzzle that floods the rooms around you!
As early as depth 10 (15 for non-out of depth spawns), kraken will appear in water and in bogs. Kraken move at the speed of eels, can seize you like bog monsters, often appear in groups, and deal large amounts of melee damage that will kill you quickly if your armour is weak and you have no means of escaping. They flee near death, regenerate quickly, and move like wraiths. Beware the Kraken!
Swimming in deep water will make items leave your backpack. However, do not fear - they will wash up on shore, and water is not a source of item deterioration in Brogue. You can either pick them up instantly if you need them now or pick them up later when the situation is safer. Be wary if the murky water borders a [chasm], as items could fall down to the next level making them harder to retrieve and destroying potions.