Over fishing, Over harvest whatever you choose to call it gets my vote along with all these other factors mentioned including ocean conditions starting with A in the alphabet of Acidification http://www.ocean-acidification.net/OAdocs/SPM-lorezv2.pdf and moving on to the other letters of the alphabet from there. I'll add disease and pollution to the list started.

Cancer harms the body when damaged cells divide uncontrollably to form lumps or masses of tissue called tumors.

IMO overfishing was the start of this cancer that began the weakening process and all the other factors or pieces of the puzzle could be the death blow if not managed correctly.

So weak, that since we have moved out of the CR to the OP I’ll add PS to the list where a quilt of woven gill nets across these tribs or rivers could and has extirpated runs of fish.