| 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 sphareophora Ehrenb., 1843 |
| Navicula spicula (Hickie) Cleve, 1894 |
| Navicula spuria Cleve, 1895 |
| Navicula stroemii Hust., 1931 |
| Navicula stundlii Hust., 1959 |
| Navicula subapiculata (Grunow) Hust., 1939 |
| Navicula subcarinata (W. Greg. ex A. Schmidt) Hendey, 1951 |
| Navicula subhamulata Grunow, 1880 |
| Navicula subinflatoides Hust., 1962 |
| Navicula subirritans Giffen, 1970 |
| Navicula subminuscula Manguin, 1942 |
| Navicula subrhynchocephala Hust., 1935 |
| Navicula subtilissima Cleve, 1891 |