| 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 |
| Navicula dirrhombus A. Schmidt, 1875 |
| Navicula discrepans A. Schmidt, 1875 |
| Navicula diserta Hust., 1939 |
| Navicula disputans R.M. Patrick, 1959 |
| Navicula distans (W. Sm.) Ralfs, 1861 |
| Navicula diversipunctata Hust., 1944 |
| Navicula diversistriata Hust., 1955 |
| Navicula duerrenbergiana Hust., 1934 |
| Navicula egena A. Schmidt, 1890 |
| Navicula eidrigiana J. Carter, 1979 |
| Navicula elegans W. Sm., 1853 |