Enhancing microalgal growth and bioactive compound production is becoming a duty for improving photosynthetic microorganisms. In this study, the growth, carotenoid, and fatty acid profiles of Conticribra weissflogii were studied under four different silicate concentrations and silicate-deficient conditions in an f/2 medium with continuous aeration, light intensity (30 ± 2 µmol m−2 s−1), salinity (25 ± 2‰), pH (8), and temperature (25 ± 2 °C). At the end of the experiment, we observed that a silicate concentration of 120 mg L−1 produced the maximum biomass dry weight (0.86 g L−1), carotenoid content (1.63 µg mL−1), and fucoxanthin content (1.23 mg g−1) in C. weissflogii. The eicosapentaenoic acid (EPA) (11,354.37 µg g−1), docosahexaenoic acid (DHA) (2516.16 µg g−1), gamma-linolenic acid (C18:3n6) (533.51 µg g−1), and arachidonic acid (C20:4n6) (1261.83 µg g−1) contents were significantly higher at Si 120 mg L−1. The results further showed the maximum fatty acid content in C. weissflogii at Si 120 mg L−1. However, the silicate-deficient conditions (Si 0 mg L−1) resulted in higher levels of saturated fatty acids (38,038.62 µg g−1). This study presents a practical approach for the large-scale optimization of biomass, carotenoid, fucoxanthin, and fatty acid production in C. weissflogii for commercial purposes.