<p>The microalgae attract attention by producing useful compounds, such as fatty acids, pigments, and biofuels, from CO₂ via photosynthesis. This process requires not only CO₂ but also water and micro- and minor nutrients. Applying seawater and marine microalgae, especially for large-scale industrial production, reduces the cost of acquiring large amounts of water for cultivation. However, the concentrations of combined nitrogen and certain metal ions, such as Fe, in the seawater are lower than in the general culture media for microalgae. We applied digester effluent from the methane fermentation as the source of these nutrients. In this study, we evaluated the application of digester effluent for cultivating a haptophyte, <i>Tisochrysis lutea</i>. At first, we confirmed the algal cells could grow by ammonium as a sole nitrogen source because ammonium was abundantly contained in the digester effluent. Then, we applied the digester effluent as a source of nutrients and found that the optimum growth was obtained when digester effluent was supplied at 2.8% (v/v) in artificial seawater. Surprisingly, the cells in this condition had increased photosynthetic pigment contents such as fucoxanthin and chlorophyll compared to those in the standard culture conditions. We surveyed ingredients in the digester effluent that could potentially increase pigment accumulation and found that iron was a critical nutrient that caused the accumulation of pigments. These findings might provide valuable information for applying digester effluent to cultivate microalgae.</p>