I worked a case one time in which a boy was murdered, his body then wrapped and weighted, and he was thrown under a bridge. The bridge also happened to be a favorite local swimming spot for teenage kids. One jumped off the bridge, went down under pretty far, and slammed into the body.
The victim had been beaten to death with metal bars and a wooden bat (drug related) and his skull had been caved in. Few things are as gruesome as discovering a bloated body underwater when you are not expecting one. It's not only horrifying, it's just plain shocking because you're not expecting it. You're swimming to have fun and come across a corpse. It leaves a real impression. Even when you're looking to find a body underwater, especially if the water is murky, it's a shock when you run into one.
Also once worked a case in which a body was to be exhumed. When the body was exhumed we found out that another body had been buried atop the one we were looking for. The body above our target was simply planted in the ground. Someone had partially uncovered the real grave and then buried the victim atop the other grave. Because of decomposition that was kinda gruesome and finding the other body was a bit of a shocker. Didn't see it coming. The backhoe tore the other body up before it was realized what was happening.
Being thrown into a narrow but deep pit and then abandoned, I've seen that too. Bad way to go. It's slow and it's got to be a helpless feeling.
Being burned alive, or forcible drowning though. Those two probably at near the top of my list.
Anything in which you know the victim suffered for along time, was particularly violent, or you know the victim near it was coming and was terrified, that's gruesome.
Dismemberment after the fact is always gruesome too, as are various methods used to attempt disposing of a corpse (improper burial, sinking, feeding remains to animals, acid, partial cannibalism, keeping trophies and body-parts, etc.)
Depends on who was doing the killing in what way, who might be secretly looking for the murderer(s) (vigilantes), and other secondary details. The players might "accidentally" run into the murderer or murderers, an accomplice, an informant, or someone looking to exact their own vengeance. Then again they could run into someone who helped cause the murder, but are unaware of their own involvement.
Me, fights along the water at night are spooky, because of the threat of drowning, being drowned by another, or injured and then having to fight my way out of the water. Water fights are exhausting anyways. I'd use a lot of ambushes, night-fights, threats from unknown adversaries, and attacks form people, creatures, and from quarters they are not at all expecting. You might think about having them surveil or follow subjects they are suspicious of into locations where they can get ambushed easily. It's what I would do to them.
The Old Light, Chopper's Isle, Lost Coast Road, a boat fight in the harbor, the swampy area, and that place that looks like a graveyard to the northeast, all good places for ambushes.
Good luck.
Edit: You know they might go out to the graveyard to see if they can find evidence of Undead activity. They dig up a body to see if the body is still in the grave because locals have seen that supposedly dead person walking around the bogs at night. As they dig up their target they find another body atop the other grave (as above). They take that body to be examined and before they can rebury it, it disappears. Later it attacks them at another location.
One thing in a situation like this you might think about and that I used one time. A Doppelganger. The sheriff, or whoever your chief law enforcement guy is happens to be is really a doppelganger. They're feeding off the situation for their own ends. So might be the familiar (if he has one) of the mage.
