The feasibility of culturing different blue Haslea species and strains in different types of photobioreactors (PBRs) was studied on the long-term (until 151 days). The different strains of blue Haslea were selected for their peculiarity to produce marennine-like blue pigments as a potential industrial high-value compound. The present study aims at assessing several factors in PBRs to obtain sustained blue pigment production in semi-continuous culture. Therefore, the effect of mixing, silicate concentration in the culture medium and type of light on marennine or marennine-like pigment production were investigated in parallel to the productivity of different Haslea strains and species. It was shown that the presence of mixing in semi-continuous PBR affected marennine production, cultures without any mixing achieving significantly higher marennine concentrations and productivities. Additionally, concentrations of silica from 45 to 75 μg L−1 in the culture medium produced higher marennine concentrations than that of 30 μg L−1. There were no significant differences in marennine production between the LEDs mixing different color and fluorescent tubes in semi-continuous PBR, thus LED could be a great option from the sustainability standpoint. Marennine production in the standard conditions used for this work was largely different between species. Haslea sp. produced the lowest pigment yields comparatively to the three H. ostrearia strains showing similar marennine productivity over 14 mg L−1. Preservation, until 155 days of marennine separated from culture supernatant and concentrated (“blue water”) was increased at low temperature (4 °C) and absence of light. This study validates the efficiency of semi-continuous systems to support long-term marennine production. However, additional work is still needed to pinpoint other factors that can further reduce the costs and result in maximum yields of marennine for industrial applications.