Negative River Stages

A river's stage at a point (a gauge reading) is not an absolute measure of the depth of the water in the channel, rather it is a depth with respect to an historical Datum level.  In summary, when a river gauge reads zero or in the negative numbers - it does not mean that the river has gone totally dry or is running below ground. It means that the gauge is reading at or below the agreed-upon zero level.

That gauge zero level is chosen considering many factors, like the USGS references (or benchmarks) that are near to the gauge site, or an historical level that may have been used for a hundred years or more. These gauge zero levels are not changed very often.

Silt may deposit in the river channel over time (filling the channel up), or the channel bottom may be scoured out to a deeper level by strong currents.

Still, the gauge zero datum levels are not changed to keep continuity.

For example, most of the gauges in the Susquehanna Basin experienced their record Flooding during Agnes in 1972. If the gauge zero level was changed on a whim, all the historical data for the gauge site could be rendered useless or at least very confusing.

For example, it may be difficult to explain to people who have been used to having a certain river level/gauge reading as a personal threshold.  They know that the water reaches the front steps of their house at 17 feet (using the current values).  If the level was to change up or down just to avoid having a negative value, it might become confusing for them to remember the new level which would impact their home.    

There is a collaboration between many government agencies in order to settle on a gauge zero, and which Datum (way of mapping the earth) will be used as a basis.

Not many sites in the region actually go below zero (Renovo and Williamsport are two examples that do). When they do go below zero, it is usually a sign of a prolonged dry spell.

In contrast, a few river gauges will not read below a certain level (which may be above it's respective gauge zero). This bottom limit/reading of these gauges is usually due to the position of the gauge in or along the river.

Some river or dam/pool water level gauges will be referred to using feet (or meters) above mean sea level (MSL). Examples of this situation are the large reservoirs in the Rockies and Western U.S. where the agencies (or power companies) have installed gauges to monitor water flows and levels.