For most river stage sites in south Louisiana, river stage is the height of the river's surface (top of the water column) relative to standard sea level. For example, at Amite/Denham Springs the river stage could be 10.2 feet - meaning that the height of the river's surface was 10.2 feet above sea level. (By comparison, Metro Airport in Baton Rouge is about 60 ft above sea level.)
And you are 100% right ... no way the Amite River is deeper than the Mississippi. At the center of the Mississippi channel, the bottom drops to something at--or even a bit below--sea level from Baton Rouge southward.
So the Amite/Denham Springs stage could be HIGHER than the Mississippi River after a flooding rain event in the Amite basin, but the Amite would never be deeper.
Now . . . I believe that EVERY site along the Mississippi River reports river stage as a measure relative to sea level, but there are some river gage locations along our local rivers that are NOT reported relative to sea level. Instead, those sites have a subjective benchmark point, often based on something historical about the local area or the river reporting practices from decades ago.
The Comite/Joor Road is not reported relative to sea level; to convert Joor Rd. readings to a sea-level relative height, you must add about 24 feet to the reported value -- I think the "correction term" actual value is 23.85 feet. So this morning's Comite/Joor Rd. report of -1.1 feet means that the river surface flow is actually about 22.75 feet above sea level.
All river stage reports along the Amite from Magnolia (EBR Parish) and Denham Springs southward are reported in values relative to sea level. But Amite gages north of Magnolia are not adjusted to sea level.
Why the discrepancies? Several reasons . . . but mostly just long-term practices that have not been changed, mainly because the locals don't want the change. I can understand that . . . these people know what a specific reading means in terms of a threat to their property, and they do not want to have to deal with the problem of converting their critical numbers to a series of new numbers.
Hope this helps!
WAFB Storm Team