| Navicula separabilis A. Schmidt, 1875 |
| Navicula serratula Grunow, 1875 |
| Navicula sigma Ehrenb., 1833 |
| Navicula silicula Ehrenb., 1843 |
| Navicula simplex Krasske, 1925 |
| Navicula simulata Manguin, 1942 |
| Navicula slesvicensis Grunow, 1880 |
| Navicula socialis T.C. Palmer. 1910 |
| Navicula soehrensis Krasske, 1923 |
| Navicula soehrensis f. capitata Krasske, 1925 |
| Navicula soehrensis f. muscicola (Petersen) Krasske, 1929 |
| Navicula sparsistriata Hust., 1964 |
| Navicula spectabilis W. Greg., 1857 |
| Navicula spectabilis var. excavata (Grev.) Cleve, 1895 |
| Navicula sphaeroptera Ehrenb., 1854 |
| Navicula sphareophora Ehrenb., 1843 |
| Navicula spicula (Hickie) Cleve, 1894 |
| Navicula spuria Cleve, 1895 |
| Navicula striolata (Grunow) Lange-Bert., 1985 |
| Navicula stroemii Hust., 1931 |