| Navicula salva A. Schmidt, 1876 |
| Navicula schmidtiana Grunow, 1876 |
| Navicula schonfeldii Hust., 1930 |
| Navicula schroeteri E. Meister, 1932 |
| Navicula schultzei Kain, 1889 |
| Navicula scintillans A. Schmidt, 1881 |
| Navicula scoliopleura A. Schmidt, 1876 |
| Navicula sectilis A. Schmidt, 1877 |
| Navicula seductilis A. Schmidt, 1874 |
| Navicula sejuncta A. Schmidt, 1874 |
| Navicula seminulum Grunow, 1860 |
| Navicula semitecta A. Schmidt, 1874 |
| Navicula separabilis A. Schmidt, 1875 |
| Navicula serratula Grunow, 1875 |
| Navicula silicula Ehrenb., 1843 |
| Navicula simplex Krasske, 1925 |
| Navicula socialis T.C. Palmer. 1910 |
| Navicula soehrensis Krasske, 1923 |
| Navicula soehrensis f. capitata Krasske, 1925 |
| Navicula soehrensis f. muscicola (Petersen) Krasske, 1929 |