Navicula incerta
is a marine microalga distributed in
Baja California, México,
commonly used in aquaculture nutrition, and has been extended to human food, biomedical, and pharmaceutical industries due to its high biological activity. Therefore, the study aimed to optimize culture conditions to produce antioxidant pigments. A central composite experimental design and response surface methodology (RSM) was employed to analyze the best culture conditions. The medium (nitrogen-deficient concentrations), salinity (PSU = Practical Salinity Unity [g/kg]), age of culture (days), and solvent extraction (ethanol, methanol, and acetone) were the factors used for the experiment. Chlorophyll
a
(Chl a) and total carotenoids (T-Car), determined spectroscopically, were used as the response variables. The antioxidant capacity was evaluated by DPPH
•
and ABTS
•+
radical inhibition, FRAP, and anti-hemolytic activity. According to the overlay plots, the optimum growth conditions for Chl
a
and T-Car production were the following conditions: medium = 0.44 mol·L
-1
of NaNO
3
, salinity = 40 PSU, age of culture: 3.5 days, and solvent = methanol. The pigment extracts obtained in these optimized conditions had high antioxidant activity in ABTS
•+
(86.2–92.1% of inhibition) and anti-hemolytic activity (81.8–96.7% of hemolysis inhibition). Low inhibition (33–35%) was observed in DPPH
•
. The highest value of FRAP (766.03 ± 16.62 μmol TE/g) was observed in the acetonic extract. The results demonstrated that RSM could obtain an extract with high antioxidant capacity with potential applications in the biomedical and pharmaceutical industry, which encourages the use of natural resources for chemoprevention of chronic-degenerative pathologies.