Nanoscale pigments (e.g., nanoscale copper phthalocyanine; nano-CuPc) are used in very large quantities on a global scale. Due to their widespread use, they may reach the aquatic environment and potentially cause environmental harm. While some focus has been on the ecotoxicity of nanopigments, studies of their bioaccumulation behaviour are still rare. To address this knowledge gap, we examined nano-CuPc bioaccumulation potential in lower trophic-level aquatic organisms exposed via both water and sediment: algae (Raphidocelis subcapitata), crustaceans (Daphnia magna) and snails (Potamopyrgus antipodarum). For the first time attachment of nano-CuPc to algae was quantified by single-cell-ICP-MS analysis after 48 hours incubation: nano-CuPc was attached to approximately 10% of the cells in the algal population. For D. magna a relatively slow uptake rate of 12.8 ng nano-CuPc per daphnia per h was found during the first 4 hours, and the rate shifted to 82.7 ng nano-CuPc per daphnia per h from 4 to 16 hours. Nano-CuPc was not found to be depurated significantly from D. magna within 24 hours in clean medium. This lack of depuration in D. magna calls for further studies with longer depuration periods to identify whether nano-CuPc accumulated in the gut epithelia or remained retained in the gut and if presence of food caused alterations. For the freshwater snail, P. antipodarum, no significant nano-CuPc concentrations were associated with tissues, shells, or total snails (i.e., tissue plus shell) after sediment nano-CuPc exposure. This is important, as our results support the finding that nano-CuPC can only be weakly dispersed in water and that sediments can be expected to be the major sink. Overall, our study showed a low bioaccumulation potential of nano-CuPc in the studied freshwater organisms suggesting a low bioavailability of sediment-associated nano-CuPc and, thus, a limited entry from sediment into the benthic food web.