One that I had driven multiple times, on SR-624/Morgan Ford Rd over the Shenandoah River, was replaced last January. Probably Virginia's busiest low water bridge while still extant, since it provided a good way to cut over to US-340/522 north from I-66 exit 13 (via Dismal Hollow Rd), without having to drive through Front Royal.
Other low water bridges in Virginia that I believe still exists:
- SR-622/Minebank Rd, Cedar Creek, north of Strasburg.
- SR-610/Bucks Mill Rd, Passage Creek, east of Strasburg. I've also driven over this one multiple times, and still sometimes think about how this was once VA-55's original routing.
- SR-635/Bowman Mill Rd, Cedar Creek, just outside Strasburg.
- SR-720/Crooked Run Rd, Crooked Run, near Bayse
- SR-667/Lupton Rd, Shenandoah River North Fork, northeast of Woodstock
- SR-609/Hollingsworth Rd, same as above, also same as above
As for fords in Virginia, I've stumbled across a few
- SR-758/George Walton Rd, North River, near Mount Solon. I haven't actually driven down this road, but I have seen the warnings about lack of turnaround space posted at both intersections on either side of the North River, which prompted me to check out satellite images of the area.
- SR-642/Lindsay Ln, Robertson River, Criglersville. Found this one by accident while trying to find a secondary road connection from US-33 to VA-231.
- SR-624/Peach Orchard Ln/Little River Rd, Black Branch/Bull Run, north of Haymarket. I can't say if this is an active ford anymore, but at one point, traffic at the formerly signalized intersection of US-15 and US-50 intersection (Gilbert's Corner) was so bad, drivers on northbound US-15 were actually fording the creek to cut over to points east. The Washington Post even did a write-up about this.
Edit: Corrected info on one crossing, added another.