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In a setting with a planet have similar atmosphere as earth with higher ocean coverage, I need a good reason for human on with equivalent of 16-17th century technology to avoid navigate through deep ocean, yet it's easy to navigate in shallow waters.
For example, It should be technically easy for most regular merchants to sail from Spain to Egypt, but from Spain to Cuba following Columbus' route should be impossible and suicidal even using the most advanced technology human have and ignoring cost. In this case I will prefer to have the depth/altitude of water being the main indicator.
Several possible way I ruled out for plot reason:
Continuous modern/future technology: I am not against higher technology as the root of cause, but such element shouldn't be a continuous effort. For example:
Good: Some nuclear war 5000 years ago left some fallout
Bad: Some Alien spaceship will shoot and sink any ship passing
And of course, I need it to be (somehow) make physical sense
Lack of destination: It's not a specific place that nobody ever been, it should be a general effect like even you know your destination is on the other side of ocean, yet you still have to do the long route in shallow water. Navigation map system should be pretty completed given the technology human has during 16-17th century.
And again just to highlight, it shouldn't be a cost/effect or risk/effect issue. Hopefully I want to create a general belief among most human that
Entering deep ocean = Death
Some visible/detectable effect that can enhance the fear is a bonus.
I have read through the question and answers here, and in this case I am not interested in making a particular area of ocean not navigable, instead I need some good reason to make the phenomenon in whole planet level, and such effect had better to be related to altitude.