I'm having slowdowns in framerate, specifically in two areas.

The first is during Mission 2 (first visit to Hell's Kitchen). A small hallway in the MJ12 sewer facility has steam coming up from some pipes and the framerate slows down as long as the steam is in my line of sight, ie not if I'm at the edge of the room, facing the door.

The second is in Missions 3 when I first enter the Mole People tunnels from Brooklyn Bridge Station. My first guess for the problem is that it's just a large open area so the game has to render/track too many characters and objects all at once but that's just a guess. The area's so big and the framerate is so bad that I haven't been able to test for specific causes as easily as one tiny room with one unique feature causing issues.

Putting aside that this is a 20 year old game and these areas ran just fine back in the day, is there a certain setting that can fix this?

Thanks.
Settings -> Display -> Detail Textures -> Off

This seems to have improved the framerate significantly in the second area.

If your hardware and OS support them, I suggest you to try installing both the replacement executable Deus Exe and the game engine Direct3D 10 renderer.