| distance | reference number | name | latitude | longitude |
| 25.0 | 1139 | Grant Line Canal (drawbridge), Old River, Californi | 37.8167 | -121.45 |
| 30.1 | 306 | Borden Highway Bridge, Middle River, San Joaquin Ri | 37.8917 | -121.488 |
| 31.1 | 2965 | Stockton, California | 37.9583 | -121.29 |
| 31.2 | 1304 | Holt, Whiskey Slough, San Joaquin River, California | 37.9333 | -121.433 |
| 32.4 | 307 | Borden Highway Bridge, Old River, San Joaquin River | 37.89 | -121.57 |
| 34.5 | 272 | Blackslough Landing, San Joaquin River, California | 37.995 | -121.422 |
| 34.5 | 2143 | Orwood, Old River, San Joaquin River, California | 37.9333 | -121.567 |
| 37.3 | 263 | Bishop Cut, Disappointment Slough, San Joaquin Rive | 38.0433 | -121.418 |
| 39.1 | 3261 | Wards Island, Little Connection Slough, San Joaquin | 38.05 | -121.497 |
| 40.2 | 1390 | Irish Landing, Sand Mound Slough, San Joaquin River | 38.0333 | -121.583 |
| 41.2 | 2449 | Prisoners Point, San Joaquin River, California | 38.0667 | -121.55 |
| 41.8 | 670 | Coyote Creek, Tributary #1, San Francisco Bay, Cali | 37.45 | -121.967 |
| 42.3 | 1116 | Gold Street Bridge, Alviso Slough, San Francisco Ba | 37.4233 | -121.975 |
| 42.5 | 3059 | Terminous, South Fork, Mokelumne River, California | 38.11 | -121.498 |
| 43.5 | 963 | False River, San Joaquin River, California | 38.055 | -121.655 |
| 44.2 | 3187 | Upper Guadalupe Slough, San Francisco Bay, Californ | 37.435 | -122.007 |
| 45.2 | 1098 | Georgiana Slough entrance, Mokelumne River, Califor | 38.1267 | -121.578 |
| 45.2 | 669 | Coyote Creek, Alviso Slough, San Francisco Bay, Cal | 37.4633 | -122.023 |
| 45.2 | 668 | Coyote Creek, Alviso Slough, San Francisco Bay, Cal | 37.465 | -122.023 |
| 45.5 | 906 | Elkhorn Slough railroad bridge, California | 36.8567 | -121.755 |
| 45.5 | 907 | Elkhorn Slough railroad bridge, Monterery Bay, Cali | 36.8567 | -121.755 |
| 45.9 | 3087 | Threemile Slough Entrance, San Joaquin River, Calif | 38.0833 | -121.683 |
| 45.9 | 1528 | Kirby Park, Elkhorn Slough, California | 36.8417 | -121.747 |
| 45.9 | 1905 | Mowry Slough, San Francisco Bay, California | 37.5 | -122.033 |
| 46.4 | 1529 | Kirby Park, Elkhorn Slough, Monterey Bay, Californi | 36.8333 | -121.75 |