The eels and kraken can pull you into the water, which can drown you very quickly, unless you have magical breathing, or are wearing a noncursed greased cloak or an oilskin cloak, in which case they cannot grab you.
Some people use the NetHack options file to replace the ; character with another, more readable one (such as 7) as a way to better distinguish a dangerous class of monsters from the water symbol.
A fun way to deal with annoying sea monsters is teleporting them out of water (or evaporating the water, if they are in a pool) and then fighting on land where their maximum HP is 1.
Because eels and kraken can drown even the healthiest of adventurers, they are best fought at a distance from the safety of land. Try to avoid standing in squares adjacent to the water so that you cannot be grabbed.
The most resource-efficient ways to dispatch sea monsters are polearms and attack spells. Polearms allow you to fight at a distance without expending any resources, but targeting can be tedious if your proficiency with polearms is less than Skilled. Attack spells can be similarly effective, so long as you have enough Energy to take out your foe.
Using projectile weapons is a less attractive tactic because the projectiles will end up falling in the water, becoming difficult to retrieve. Throwing daggers at sea monsters is highly inadvisable for this reason.
Another good tactic is to wear a MC3 cloak, to carry an escape item, and to melee them. On those few occasions when an eel can successfully swing itself around you, you have one guaranteed turn to teleport it away or to engrave a single Elbereth into the ground with an athame, wand of fire, lightning, or digging. However, you should make sure you are not impaired in order to ensure 100% success.
Finally, simply running away is also a viable strategy, especially on the Plane of Water.