Here's something simple that would improve clearance.
There is a short aqua straight track section (looks like about 6 inches in length) at the lower end of your aqua S-curve that leads onto the bridge. Remove that aqua section to move the entire aqua S-curve downwards in your diagram and insert that same straight aqua section at the top of the aqua S-curve. Similarly, on the yellow S-curve, remove the short yellow straight track section at the top of your diagram and put it at the bottom of the yellow S-curve leading onto the bridge. Those changes will move the two S-curves further apart and will increase the clearance. Lay the tracks and check the actual clearance with locomotives and cars before you finalize the track locations.
MELGAR