With the development of nanotechnology, titania nanoparticles play a significant role in biomedical environmental applications. With the aim of better understanding bio-matrix/nanoparticle surface interactions, studying the influence of amino acids on the colloidal behavior of nanoparticles may provide valuable insights into the formation of the protein corona. In water nanoparticles, surface reconstruction and aggregation are determined to be different under varying pH levels and the presence of amino acids. However, there are not enough data to predict the influence of amino acids on the stability of anatase and rutile nanoparticles in the same conditions. In our work, we examined the colloidal properties of anatase and rutile nanoparticles, with an average size of 26 and 102 nm, respectively, and showed that the addition of five amino acids with contrasting surface charges (glutamic acid, cysteine, glycine, lysine, and arginine) enhances the aggregation of particles in an aquatic medium. In this work, we measured particle size distribution and zeta-potential in suspension with pH values ranging from 3 to 11. It has been revealed that under the same conditions, rutile nanoparticles have a lower pH dependence of the aggregation state compared to those of anatase, which are always more aggregated than rutile nanoparticles. The presence of amino acids tends to shift the pH of the isoelectric point of surface toward acidicity. For the particles in glutamic acid, glycine, and lysine, the highest degree of aggregation is achieved reasonably at a pH close to that of the isoelectric point. A contrasting effect of pH on the behavior of rutile and anatase nanoparticles was found in cysteine and arginine. Our findings showed that in an acidic medium (pH 3–5), aggregation depends more on pH; in a weakly acidic medium (5–7), it depends on the surface of the particles; and in an alkaline medium (7–11), on the nature of the amino acids.