short stories - A horror story set onboard a ship about a man whose roomate is anything but human who proceeds to terrify him as he fears for his life and his sanity

Sailing to his destination,.he beds down for the night. He is awakened by his room mate running from the room and racing down the hall. He notices that the porthole hatch, or round window, is open even though it hadn't been open when he went to bed, And is accompanied by a terrible smell, like decaying sea weed or water. He learns that the man from his room has fallen or jumped overboard. He talks the ship captain into helping him by staying a night in the room.

Answer

This is The Upper Berth by F. Marion Crawford. It's pretty famous as old-timey ghost stories go, and has been in dozens of horror anthologies. It's exactly as you described - a man at sea sleeping in a lower berth is troubled in the night, though not as badly as his roommate in the upper berth:

I was sleeping soundly when I was suddenly waked by a loud noise. To judge from the sound, my room-mate must have sprung with a single leap from the upper berth to the floor. I heard him fumbling with the latch and bolt of the door, which opened almost immediately, and then I heard his footsteps as he ran at full speed down the passage, leaving the door open behind him. The ship was rolling a little, and I expected to hear him stumble or fall, but he ran as though he were running for his life. The door swung on its hinges with the motion of the vessel, and the sound annoyed me. I got up and shut it, and groped my way back to my berth in the darkness. I went to sleep again; but I have no idea how long I slept.

When I awoke it was still quite dark, but I felt a disagreeable sensation of cold, and it seemed to me that the air was damp. You know the peculiar smell of a cabin which has been wet with sea water. I covered myself up as well as I could and dozed off again, framing complaints to be made the next day, and selecting the most powerful epithets in the language.