| Navicula cryptocephala var. cryptocephala Kütz., 1844 |
| Navicula cryptocephala var. genuina Cleve-Euler, 1953 |
| Navicula cryptocephala var. intermedia Grunow, 1880 |
| Navicula cryptocephala var. perminuta (Grunow) Cleve, 1895 |
| Navicula cryptocephala var. subsalina Hustedt, 1925 |
| Navicula cryptocephala var. veneta (Kütz.) Rabenh., 1822 |
| Navicula cryptotenella Lange-Bert., 1985 |
| Navicula cuspidata (Kütz.) Kütz., 1844 |
| Navicula cuspidata var. cuspidata (Kütz.) Kütz., 1844 |
| Navicula dalmatica Grunow, 1860 |
| Navicula decipiens Castrac., 1886 |
| Navicula dicephala Ehrenb., 1838 |
| Navicula didyma (Ehrenb.) Kütz., 1844 |
| Navicula diffusa A. Schmidt, 1874 |
| Navicula digito-radiata (W. Greg.) Ralfs, 1861 |
| Navicula diplosticta Grunow, 1875 |
| Navicula directa (W. Sm.) Ralfs, 1861 |
| Navicula directa var. directa (W. Sm.) Ralfs, 1861 |
| Navicula directa var. remota (Grunow) Cleve, 1895 |
| Navicula directa var. subtilis (W. Greg.) Cleve, 1883 |