I don't understand your edits to bridges. You can map a bridge as an area (man_made=bridge) but when doing so you shouldn't remove bridge=yes and layer=1 from highway that crosses the bridge. Also, where road and river intersect there's normally either a bridge or a culvert, not both together, and usually there is no need adjust layer for both road and river (normally set only layer=1 for bridge, and layer=-1 for culvert).

There are also some problems with landcover, you drew a marsh that overlaps with water, and also it appears that water area for Põltsamaa river is currently broken (relation not closed).

Possibly this changeset should be reverted.

As for drains, I'd also consider using waterway=ditch for that small waterways, eventhough they are probably natural.