A small unidentified species of Navicula was observed in sandy sediments of a Quaternary spring near Lodz in Central Poland. The species was thoroughly analyzed using light (LM) and scanning electron (SEM) microscopy. It was compared to established species of Navicula from available published sources and its assignment to an established taxon was unsuccessful. Hence, we decided to describe it as a species new for science and the name Navicula fontana sp. nov. is proposed. Navicula fontana sp. nov. was compared to several established species, e.g. N. microdigitoradiata, N. meulemansii, in terms of size dimension range, morphology, ultrastructure, and autecology. Firstly, it differs in terms of autecology living in freshwater, whereas the others thrive in brackish water habitats. Although the type habitat of N. fontana sp. nov. is in a spring, we also observed it in headwaters of rivers with high water quality.