Web GIS Systems
In recent years, government agencies such as the USGS and many states have started to make GIS information available over the Internet.
All of the systems allow you to zoom to a location and render a custom map that clearly highlights the information that you care about. Often, you'll want to use this in combination with other systems such as topo maps (so you can initially locate the stream using their indexes).
Most of the systems work similarly (indeed, most are built using software provided by the market leader in GIS technology, ESRI). You customize the map by selecting the "layers" you want. For example, in most systems "streams" are a separate layer. In fact, you'll often streams segmented into several layers. Typical layers might be called: "Major streams", "100K Streams" - which encode the streams shown on USGS 1:100,000 survey maps, and "25K Streams", i.e. those streams shown on the 1:25,000 maps. Similarly, lakes and ponds are typically found in a separate layer called "water bodies".
NHD Geodatabase
One of the most useful viewers is provided by the USGS, originally intended to support environmental water quality regulation (making it fantastically useful for fishermen). It can be found at http://nhdgeo.usgs.gov/viewer.htm Here we show a typical view, based on selection of a gray-scale base map, and medium resolution streams (called "NHD flow lines" for reasons known only to the USGS - most other systems name their layers more intuitively).
The tools on the left hand side of the browser allow you to control the location and scale of the map. The layers are selected by checking boxes on the right hand side (many more layers are available by expanding the different categories). The next screen shows the same view, but with the "high res" streams checked.
One of the most powerful features of this viewer is its ability to generate beautifully labeled, custom road maps. (Keep in mind the target users for this system were environmental workers who often need to drive to these streams, just like fishermen. Maps can be printed up to 32"x44". A small segment of one of these print images is shown below.
A PDF containing a sample print image of a complete map is here.
Eastern Brook Trout Joint Venture Advanced Web Mapper
For the fly fisherman, one of the most exciting viewers came out this year from the EBTVJ. It provides information about brook trout habitat coded at the HUC level 6 watershed (pretty small). Not every stream within a drainage will hold trout to the same extent, but the majority will. It also shows waterbodies roughly corresponding to the USGS 100K map series...all but the smallest streams worth fishing will be found here directly, and of course you can compare the drainages with the 50K and 25K series topo maps to discover more (or the NHD viewer, if you select the highest level of detail).
To get to the viewer you can go to:
and select the "Maps" tab. You'll come to a screen like this:
Select the "Use the Advanced Web Mapper" link. For this to work, you may need to allow pop-ups. A new window will open up which contains the map viewer. After a few seconds, you'll see a window that shows the entire extent of the native eastern brook trout range:
This is a pretty standard web viewer. You can zoom in on any area you wish to see details:
Color coding is as follows:
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Green areas are places where brook trout populations are intact (best)
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Yellow, where brook trout are somewhat diminished (good)
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Red, where brook trout are greatly diminished (not so good)
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Blue, brook trout exist, but no quantitative data (your guess)
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Mottled purple, no data (your guess)
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Dark gray, extirpated (no brook trout, though wild trout of other species are still possible)
Keep in mind that brook trout can be diminished by other trout species, so some red or even gray areas may be excellent wild brown or rainbow water. But it's almost certain that the yellow and green areas are great places to find wild trout.
MassGIS
The Commonwealth of Massachusetts provides a very nice java-based viewer called MassGIS - OLIVER, along with a huge array of information about the commonwealth. The viewer is available for free download from here:
http://www.mass.gov/mgis/mapping.htm
For example, below we see a layer of "bedrock lithology". While it's not all that useful at this scale, think about zooming in, and overlaying a stream layer. If the bedrock is limestone, and there's a stream running through it, you've found a limestone stream.
Unfortunately, MassGIS covers only Massachusetts. It also uses an XY coordinate system that's expressed as meters from a reference point, rather than longitude and latitude. That makes it harder to use in conjunction with other systems such as Google Earth. It is possible to convert from the MA coordinate system to Long/Lat using free software provided by the US Army Corps of Engineers, here:
http://crunch.tec.army.mil/software/corpscon/corpscon.html
Other States
New Jersey has a web-based GIS viewer. However, I find it doesn't work very well. Data layers are segmented by the department which provides the data. As a result, you can't overlay roads (which are owned by DOT, and available on the DOT version of the viewer), with streams (which data is provided by EDA).
I find in NJ you're better off either using the USGS viewer, or downloading GIS databases (which are freely available), and viewing them locally using ArcExplorer (see GIS Data section).
The PA Fish and Boat Commission has a viewer specifically targeted to wild trout streams. See discussion in the PA stream page.
NY doesn't have an online viewer (or at least not one I've found). Frankly, I haven't yet looked for other states. Try a Google search on:
[State Name] GIS viewer
and you'll probably come up with it, if it exists.