The two men enjoy their ride down the river, passing towns along the way. Getting supplies in a small village they are warned that no one goes into the area they are headed to, but they go anyway. Soon they reach a deserted area, and stop at an island for the night. Setting up camp, they have uneasy feelings about the place, and especially the swaying small trees covering the island, feeling as though they were alive. At dusk, they see a man come down the river standing up in his boat, odd to see at dusk. The man gestures wildly at them and further spooks them, but when they see a creature floating down the river that looks like a body- real fear sets in. Further developments add to the horror as a terrifying climax is reached that endangers their lives and sanity
I am going to guess Algernon Blackwood's "The Willows".
Two friends are midway on a canoe trip down the Danube River. Throughout the story Blackwood personifies the surrounding environment—river, sun, wind—and imbues them with a powerful and ultimately threatening character. Most ominous are the masses of dense, desultory, menacing willows, which "moved of their own will as though alive, and they touched, by some incalculable method, my own keen sense of the horrible."
At one point the two men see a man in a "flat-bottomed boat". However, the man appears to be warning the two, and ultimately crosses himself before hurtling forward on the river, out of sight. During the night and into the next day and night, the mysterious, hostile forces emerge in force, including large, dark shapes that seem to trace the consciousness of the two men, tapping sounds outside their tent, shifting gong-like sounds, and the appearance that the willows have changed location. In the morning the two discover that one of their two paddles is missing, there is a slit in the canoe that needs repair, and some of their food has disappeared.
They find the corpse of a peasant lodged in roots near the shore. When they touch the body, a flurry of living presence seems to rise from it and disappear into the sky, and later they see the body is pockmarked with funnel shapes as had been formed on the sands of the island during their experience. These are "Their awful mark!" the Swede says. The body is swept away, resembling an "otter" they thought they had seen the previous day, and the story ends.
You can find links to the Project Gutenberg copy of the story, as well as a Librivox recording, at the bottom of the Wikipedia page.