What the OP is suffering from is an IRRATIONAL fear. You will not become sick from bathing in the ocean or in a lake, therefore there is nothing to fear, but even so, let me try to soothe you.
Lakes and oceans have natural "filtration" systems. For example, all the fish feces and other such things are eventually eaten by bacteria or sinks to the bottom of the ocean, where it is covered by yet more sediment and eventually ends up sliding under a tectonical plate, where it eventually turns into rocks and minerals.
Of course, not all oceans have such a place where two tectonical plates collide, but the fish feces and fish blood, and so on, either sinks to the bottom or is eaten by bacteria. The point is that particles of ANYTHING organic cannot "accumulate" for millions of years. Organic matter has the small side-effect of ROTTING.
Therefore you would not be "swimming with millions of years of fish feces, fish blood and decomposed flesh" if you decided to take a dip in the ocean.