Aquatic toxicology of engineered nanoparticles is challenged by methodological difficulties stemming partly from highly dynamic and poorly understood behavior of nanoparticles in biological test systems. In this paper scientific and technical challenges of testing not readily soluble nanoparticles in standardised algal growth inhibition tests are highlighted with specific focus on biomass quantification methods. This is illustrated through tests with TiO2 and Au nanoparticles, for which cell-nanoparticle interactions and behavior was studied during incubation. Au NP coating layers changed over time and TiO2 nanoparticle aggregation/agglomeration increased as a function of concentration. Three biomass surrogate measuring techniques were evaluated (coulter counting, cell counting in haemocytometer, and fluorescence of pigment extracts) and out of these the fluorometric methods was found to be most suitable. Background correction was identified as a key issue for biomass quantification, complicated by algae-particle interactions and nanoparticle transformation. Optimisation of the method is needed to reduce further particle interference on measurements.