If you have the Network Analyst extension I think you might find that it is easiest to use the Origins Destinations (OD) Cost Matrix tool. I have done this for several instances like this and it works well. You do need to create a network dataset using fish locations as point data and then your stream(s) as your line data. ESRI has a nice overview of the tool here: http://resources.arcgis.com/en/help/main/10.1/index.html#//00480000000m000000
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