Heart of Darkness is very dense with symbolic language and themes, and much of Marlow's story is not intended to be literal but instead an evocation of the feelings he gained from traveling into the jungle. One good example is Marlow's shoes; after the helmsman is killed, Marlow's shoes are filled with his blood and Marlow becomes desperate to get them off.
To tell you the truth, I was morbidly anxious to change my shoes and socks. 'He is dead,' murmured the fellow, immensely impressed. 'No doubt about it,' said I, tugging like mad at the shoe-laces. 'And, by the way, I suppose Mr. Kurtz is dead as well by this time.'
(Conrad, Heart of Darkness, gutenberg.org)
Marlow's discomfort is not only because his shoes are full of blood, but because he has just become fully aware of the fragile state of human life in the jungle. He links the dead helmsman to his shoes, and links his shoes to Kurtz, and is convinced that Kurtz is already dead. Flinging his shoes overboard is, to Marlow, an act of rebellion; he wants to meet Kurtz and feels that having the physical proof of death right there on his feet could somehow hurt his chances. For Marlow, his shoes are an unacceptable proof that death is real and even inevitable; he moves past them later, and finds himself unable to explain his real feelings about the event to his audience.