This study assesses the temporal changes in the physico-chemical behaviour of titanium dioxide nanoparticles (anatase and rutile phase) for a period of 120 h at environmentally relevant concentration of 1,000 µg/L, and the consequent impact on the microalgae population in a fresh water microcosm. The mean hydrodynamic size analysis in the medium revealed the differences in the aggregation behaviour of the two crystalline types of particles within first 12 h exposure before they had reached the micron size range. While the short term exposure (120 h) showed an immediate effect on the resident microalgae in the microcosm with respect to control, there were no significant differences in ecotoxicity effects of rutile and anatase phases of titania. The long term (90 days) exposure demonstrated a gradual recovery of the resident algal population. Summarizing the observations, the nanosized particles at low concentration may not retain the toxic potential for longer exposure time in a microcosm presumably owing to the complexity prevalent in the natural systems. © 2014, The National Academy of Sciences, India.