PTAGIS always wants to know LLID and river kilometer for tagging or detection locations. To help my team at Yakama Nation Fisheries, I always query the old SSHIAP layer routes with ArcMap and the Identify Route Locations. Sometimes I am able to overlay their point feature classes on SSHIAP classes to get the route measures and LLID for a batch of points. The NHD stuff doesn't seem very useful for stream identification, because it doesn't preserve the LLID number, and not so useful for stream kilometer, because the routes are broken up into smaller reaches.
Lately, I have been thinking about how I might provide a tool so people in my team, and others in the Pacific Northwest who are tagging fish can look up this info for themselves, particularly for those that don't have ArcGIS Desktop. Perhaps a web app. Some people use my ArcServer services in Google Earth as overlays, but I don't think Google Earth can serve route locations. Is it even possible to deliver something like Identify Route Locations data from a GIS Pro App, GIS Online, or ArcServer map service? I have a couple instances of ArcServer 10.3.1 running here, so maybe I could test this.
Not entirely sure I completely understand what output information the end user would be interested in receiving, but it sounds like a linear referencing problem. You could look into the LR toolset for a tool that meets your needs, as all of them can be published as GP services that can be used in web apps. For example, you can have a feature set, have the end user digitize a point or points, pass those as input to the Locate Features Along Routes tool along with other necessary parameters, and return information about the m-values of the points.