You had a crap ton of illegal dumping and for years even legal release of all sorts of crap. One of the biggest issues was that for years the assorted packing plants could lease blood etc. directly into the river. Ironically, the Trinity is one of the most positively impacted water bodies from the Clean Water Act. The passage in '72, and the '77 and '87 amendments had a huge impact on the Trinity. Changes in stormwater management have also helped some (also largely driven by the CWA).
There are still issues of course. There is very little protection of the Trinity headwaters areas, and then it quickly runs through the Metroplex. There is still illegal dumping, but the Dallas Marshalls are pretty decent at pursuing those. I have shown up at Joppa Preserve at 6 AM to scout for pigs, and found 15 leaking barrels sitting in the parking lot with unknown substances (used motor oil). A nature photographer volunteer I work with caught 3 guys dumping GALLONS (like 3 truckbeds worth) of paint and thinner straight into the lake. Right now I am working on issues related to an old hexavalent chromate and cadmium plating facility that was in operation for 90 plus years. It has been proposed as a Super Fund site, so you can imagine the fun politics of that. There is a creek that runs straight from the old plant to the Trinity. They are still trying to figure out the level of contamination involved. Yet, any given day, where that creek meets the Trinity is a very popular fishing spot (gag). For 4 years I worked on various aspect of the bacterial TMDLs as they relate to wildlife (aka why aggressive feral hog trapping is listed as a bacterial load BMP).
We have a lot to improve on the Trinity, and have come a long way, and the otters are a great indicator that things have improved.