| Navicula ruttneri Hustedt, 1936 |
| Navicula sabiana R.M.Patrick, 1959 |
| Navicula salinarum Grunow, 1880 |
| Navicula salinarum var. intermedia (Grunow) Cleve, 1895 |
| Navicula salinarum var. salinarum Grunow, 1880 |
| Navicula salinicola Hust., 1939 |
| Navicula salva A. Schmidt, 1876 |
| Navicula schmidtiana Grunow, 1876 |
| Navicula schoenfeldii 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 seibigiana Lange-Bert., 1993 |
| Navicula sejuncta A. Schmidt, 1874 |
| Navicula seminuloides Hust., 1937 |
| Navicula seminulum Grunow, 1860 |
| Navicula semitecta A. Schmidt, 1874 |