| 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 |
| Navicula suchlandtii Hust., 1943 |
| Navicula suspecta A. Schmidt, 1875 |
| Navicula tackei Hust., 1942 |
| Navicula takoradiensis Hendey, 1958 |
| Navicula taraxa M.H. Hohn & Hellerman, 1966 |
| Navicula tenella Bréb., 1849 |
| Navicula tenera Hust., 1937 |