Not sure how important this is though as I have a fishing hole with the water @ Y=58 with which I've not had this problem.
It is, however, under a large pond with a glass light pipe reaching up through the water. [I suspect this is because the water mob cap (of 5) fills whle I'm approaching the farm, removing armor, etc. ])
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WARNING: I have an extemely "grindy" playstyle; YMMV — if this doesn't seem fun to you, mine what you can from it & bin the rest.
If you are having the kraken appear, this probably means MCMMO is installed on the server and therefore afk fish farms will not work (the kraken gets summoned as a fishing event and therefore won't follow normal spawning rules).
My suggestion is to just maintain a large supply of normal/cheap rods and let the kraken break what it wants.