After a nice swim in the large "to some island" underwater zone, I experienced permanent movement reduction that no amount of resting, relogging, antidotes, or restoration would cure. It was either due to the water slowing, or the multiple slow bolts I ate from a few irritating little detritivore slugs.
So, one of those two caused this persistent run speed loss.
Yeah this has happened to me after swimming somewhere else, I imagine a reset will fix it or a DM killing and reviving you works.
I've just had this bug occur as well - yet I've been under the same circumstance as the op before and not had this happen. Very odd.
Simply just returning to the underwater area for a moment fixed this for me.