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| San Joaquin River is one of the most polluted rivers in the United States, especially in its lower course. Years of pesticides and fertilizers being applied to the surrounding lands as well as municipal runoff have led to elevated levels of selenium, fluoride, nitrates and other substances in the river and its tributaries; pesticide pollution is now considered "ubiquitous" to the San Joaquin River system. |
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| Fish Species | | |
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| Bass, Striped | | Sturgeon, White |
| Pikeminnow, Sacramento | | Trout, Rainbow |
| Sculpin, Prickly | | Lamprey, River |
| Chub, Thicktail | | Splittail |
| Sculpin, Riffle | | Stickleback, Threespine |
| Sculpin, Pacific Staghorn | | Sucker, Sacramento |
| Lamprey, Western Brook | | Hardhead |
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| Salmon, Chinook | | Smelt, Delta |
| Smelt, Longfin | | Lamprey, Kern Brook |
| Dace, Speckled | | Perch, Sacramento |
| Hitch | | Lamprey, Pacific |
| California Roach | | Sacramento Blackfish |
| Chum Salmon | | Perch, Tule |
| Sturgeon | | |
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