Synthetic dyes play a fundamental role in the textile industry and in laboratories engaged in teaching and research. However, their treatment and final disposal pose significant challenges due to the complex structures of these compounds, which are difficult to degrade using conventional methods. As a result, they often generate considerable environmental impact. A promising alternative for efficiently managing dye waste and mitigating its environmental effects is the use of biological treatments with microalgae, which stands out for its cost-effectiveness and high efficiency in degrading chemical dyes. In this context, the present research evaluated the removal capacity of two synthetic dyes—methylene blue and crystal violet—in aqueous solutions using the microalgae Chlorella sorokiniana and Arthrospira platensis. A 23 factorial design was implemented, including three factors with two levels each, resulting in eight treatment combinations. The factors considered were dye type (methylene blue or crystal violet), microalgae species (C. sorokiniana or A. platensis), and aeration condition (with or without aeration). In addition, the research included negative controls, and each treatment was performed in triplicate. The results showed that A. platensis achieved a removal efficiency of 99.99% for crystal violet with aeration and 99.68% without aeration. For methylene blue, A. platensis reached a removal efficiency of 97.28% under aerated conditions, highlighting its strong potential for dye removal. In comparison, C. sorokiniana removed 95.50% of crystal violet and 95.15% of methylene blue with aeration.