Seine River water was used as a natural environmental medium to quantify the ecotoxicological impact of three types of manufactured titanium dioxide (TiO2) nanoparticles toward the model bacterium Escherichia coli. Under ambient light, a significant toxicity starting at 10 ppm of TiO2 in water was observed. Presence of the anatase polymorph slightly increased the toxicity in comparison to pure rutile samples. Furthermore, the toxicity was found to be lower at pH 5 compared to Seine water (pH 8). To assess the nanoparticles state of dispersion and their interactions with bacteria, cryogenic transmission electron microscopy (TEM) and zeta potential measurements were performed. A higher sorption of nanoparticle aggregates on cells is observed at pH 5 compared to Seine water. This allows concluding that the observed toxicity is not directly linked to the particles sorption onto the cell surfaces. In spite of stronger interaction between cells and nanoparticles at pH 5, a bacterial subpopulation apparently non-interacting with nanoparticles is evidenced by both TEM and zeta potential measurements. Such heterogeneities in cell populations can increase global bacterial resistance to TiO2 nanoparticles