Right so this kind of thing gets dismissed too quickly and it really shouldn't. Creeks and waterways are genuinely underlooked habitats when it comes to mystery animal reports, especially at night when most people aren't paying attention.
Few questions though - how big are we talking roughly? Like dog-sized or bigger? And was it making any noise or just moving silently through the water? Silent movement in my experience is actually more unsettling than something that's splashing about, it suggests something that knows what its doing.
Also whereabouts are you located? Not asking for your exact address obviously, just general region because that changes things considerably in terms of what it could plausibly be. A mystery creek creature in the American south is a very different conversation to one in say, Scotland.
Have you gone back in daylight to check for tracks or disturbance in the mud? That would be the first thing I'd do. Even a partial print tells you a lot. Post photos if you find anything, even if they're not great quality - people on here are good at pulling detail out of bad images.