There are a number of major sources of river flow information in the USA and numerous sources that have flow information about a few or even just one river. USGS Gauges The USGS is the major national source of flow information along with rainfall, groundwater and surface water information. American Whitewater has long been able to link to and utilize USGS real time river flow information in our river web pages. Rainfall information can also be important for many streams. USGS also stores historical information about a great many rivers. At the end of each water year almost all gauge data is reported to the USGS as daily averages. USGS makes that daily data public about 6 to 9 months after it is reported. Over the years many rivers have had multiple gauges located at different points. USGS stores the data from all of those gauges including statistics, location information and years of operation. Boaters and river stewards can study the information from those historical gauges and learn a great deal about a watershed. Real time USGS gauges usually report every 15 minutes and so provide a very good record of daily and hourly fluctuations in flow. However, after about 3 months, USGS only displays daily data. It is unclear whether the 15 minute data is actually discarded or not, but it seems quite probable. If you need 15 minute data for a reach, you need to store that data yourself before it expires.
CDEC California Data Exchange Center, is the major river flow information source besides USGS in California. CDEC gauges report in 15 minute intervals and the 15 minute data seems to be stored in the historical archives as well. However, most CDEC historical data only goes back a few years. Older data is usually only available from USGS. The CDEC interface has gone through major upgrades and a great variaty of information can be found there besides river flows. Rainfall, surface storage, snow packs and other data are made available by CDEC.
Army Corp of Engineers This agency operates a number of dams and reservoirs across the USA. The tend to provide hourly inflow and outflow information for their reservoirs and they often have stream gauges upstream or downstream of their projects as well. As of 2008 their flow information interfaces tend to be simple tables and they usually only show flow information for 7 days or so. Historical flow information for Army Corp gauges is stored by USGS and is available half a year after the end of each water year.