In the safety and efficacy assessment of novel nanomaterials, the role of nanoparticle (NP) kinetics in in vitro studies is often ignored although it has significant implications in dosimetry, hazard ranking and nanomedicine efficacy. Here, we demonstrate that certain nanoparticles are buoyant due to low effective densities of their formed agglomerates in culture media, which alters particle transport and deposition, dose-response relationships, and underestimates toxicity and bioactivity. To investigate this phenomenon, we determined the size distribution, effective density, and assessed fate and transport for a test buoyant NP (polypropylene, PP). To enable accurate dose-response assessment, we developed an inverted 96-well cell culture platform in which adherent cells were incubated above the buoyant particle suspension. The effect of buoyancy was assessed by comparing dose-toxicity responses in human macrophages after 24 h incubation in conventional and inverted culture systems. In the conventional culture system, no adverse effects were observed at any NP concentration tested (up to 250 μg ml−1), whereas dose-dependent decreases in viability and increases in reactive oxygen species were observed in the inverted system. This work sheds light on an unknown issue that plays a significant role in vitro hazard screening and proposes a standardized methodology for buoyant NP assessments.