| distance | reference number | name | latitude | longitude |
| 39.1 | 2965 | Stockton, California | 37.9583 | -121.29 |
| 42.8 | 1139 | Grant Line Canal (drawbridge), Old River, Californi | 37.8167 | -121.45 |
| 45.2 | 1304 | Holt, Whiskey Slough, San Joaquin River, California | 37.9333 | -121.433 |
| 46.7 | 272 | Blackslough Landing, San Joaquin River, California | 37.995 | -121.422 |
| 46.8 | 306 | Borden Highway Bridge, Middle River, San Joaquin Ri | 37.8917 | -121.488 |
| 48.3 | 263 | Bishop Cut, Disappointment Slough, San Joaquin Rive | 38.0433 | -121.418 |
| 51.1 | 307 | Borden Highway Bridge, Old River, San Joaquin River | 37.89 | -121.57 |
| 52.1 | 2143 | Orwood, Old River, San Joaquin River, California | 37.9333 | -121.567 |
| 52.3 | 3261 | Wards Island, Little Connection Slough, San Joaquin | 38.05 | -121.497 |
| 54.5 | 3059 | Terminous, South Fork, Mokelumne River, California | 38.11 | -121.498 |
| 55.4 | 2449 | Prisoners Point, San Joaquin River, California | 38.0667 | -121.55 |
| 56.0 | 1390 | Irish Landing, Sand Mound Slough, San Joaquin River | 38.0333 | -121.583 |
| 58.9 | 1976 | New Hope Bridge, Mokelumne River, California | 38.2333 | -121.483 |
| 58.9 | 1098 | Georgiana Slough entrance, Mokelumne River, Califor | 38.1267 | -121.578 |
| 60.3 | 963 | False River, San Joaquin River, California | 38.055 | -121.655 |
| 60.9 | 2836 | Snodgrass Slough, Sacramento River, California | 38.275 | -121.487 |
| 62.6 | 3087 | Threemile Slough Entrance, San Joaquin River, Calif | 38.0833 | -121.683 |
| 63.3 | 2953 | Steamboat Slough, Snug Harbor Marina, Sacramento Ri | 38.2 | -121.612 |
| 64.3 | 3088 | Threemile Slough, Sacramento River, California | 38.1067 | -121.7 |
| 65.1 | 2547 | Rio Vista, Sacramento River, California | 38.1467 | -121.69 |
| 67.8 | 80 | Antioch, San Joaquin River, California | 38.02 | -121.815 |
| 68.5 | 581 | Clarksburg, Sacramento River, California | 38.4167 | -121.517 |
| 70.3 | 906 | Elkhorn Slough railroad bridge, California | 36.8567 | -121.755 |
| 70.3 | 907 | Elkhorn Slough railroad bridge, Monterery Bay, Cali | 36.8567 | -121.755 |
| 70.4 | 670 | Coyote Creek, Tributary #1, San Francisco Bay, Cali | 37.45 | -121.967 |