Navicula incerta is a benthic diatom with potential use in nutrition and health for humans and aquaculture. Therefore, it is important to know its optimal growth conditions and biochemical composition. In this study, the effects of nitrate and silicate concentration on the growth kinetics and biochemical composition of N. incerta under laboratory conditions were measured. F/2 media was used as the control, and different concentrations of nitrogen (N/4, N/8 and N/16) and silicates (Si/4, Si/8 and Si/16) were evaluated. We measured cell concentration, chlorophyll-a and conducted proximal chemical analyses. It was found that different concentrations of nutrients affected the diatom’s growth kinetics and affected the concentrations of ash, chlorophyll, protein, lipids and carbohydrates. The highest concentration of lipids was obtained in the limiting treatment of nitrogen N/8 (27.09%), while the lowest value was found with silicate Si/8 media (16.97%). Carbohydrates increased compared to the control, with the N/16 treatment presenting the maximal concentration (23.31%). Treatments with reduced nitrate (N/8 and N/16) demonstrated the lowest concentrations of protein (18.75 and 12.44%, respectively), while in reduced silicate treatments, no statistical differences (P ≥ 0.05) were observed. Therefore, media limited nitrogen and silicates affected the growth kinetics and proximal chemical composition of N. incerta. The growth of this species using the N/8 medium is a suitable method for increasing lipid concentration in N. incerta.