RivEX has a tool for extracting out nearby network in an upstream direction starting from a point snapped the the base river network. So as long as your network conforms to RivEX requirements, you could extract out the end points of your critical habitat network, ensure these are snapped to the base network and run them through RivEX. The RivEX manual provides worked examples, have a look at these to get an idea of what the tool is capable of.
