In natural environment, the microorganisms are exposed to complex mixtures of contaminants, including manufactured nanoparticles and their aggregates. Evaluation of the toxicant accumulation in biota exposed to such cocktails is a challenging task because the microorganisms need to be separated from nanomaterial aggregates often of a comparable size. We propose a method for separation of TiO
2
aggregates from green microalga
Chlamydomonas reinhardtii
and subsequent determination of cellular Hg concentration in algae exposed to mixture of Hg with nanoTiO
2
, known also to adsorb Hg. The method is based on differences in specific weight of algae and TiO
2
aggregates, using medium speed centrifugation on a step gradient of sucrose. The efficiency of the separation method was tested with nanoTiO
2
of three different primary sizes at four concentrations: 2, 20, 100 and 200 mg L
−1
. The method gives a possibility to separate nanoTiO
2
and their aggregates from the algae with a mean recovery of 83.3% of algal cells, thus allowing a reliable determination of Hg accumulation by microalgae when co-exposed to Hg and nanoTiO
2
.
• A rapid and reliable method to separate algal cells and nanoparticle aggregates of comparable size.
• A method to measure the cellular amount of Hg in green alga co-exposed to Hg and nanoTiO
2
.