To date, research on the toxicity and potential environmental impacts of nanomaterials has predominantly focused on relatively simple and single-component materials, whilst more complex nanomaterials are currently entering commercial stages. The current study aimed to assess the long-term and size-dependent (60 and 500 nm) toxicity of a novel core–shell nanostructure consisting of a SiC core and TiO
2
shell (SiC/TiO
2
, 5, 25, and 50 mg L
−1
) to the common model organism
Daphnia magna
. These novel core–shell nanostructures can be categorized as advanced materials. Experiments were conducted under environmentally realistic feeding rations and in the presence of a range of concentrations of humic acid (0.5, 2, 5, and 10 mg L
−1
TOC). The findings show that although effect concentrations of SiC/TiO
2
were several orders of magnitude lower than the current reported environmental concentrations of more abundantly used nanomaterials, humic acid can exacerbate the toxicity of SiC/TiO
2
by reducing aggregation and sedimentation rates. The EC
50
values (mean ± standard error) based on nominal SiC/TiO
2
concentrations for the 60 nm particles were 28.0 ± 11.5 mg L
−1
(TOC 0.5 mg L
−1
), 21.1 ± 3.7 mg L
−1
(TOC 2 mg L
−1
), 18.3 ± 5.4 mg L
−1
(TOC 5 mg L
−1
), and 17.8 ± 2.4 mg L
−1
(TOC 10 mg L
−1
). For the 500 nm particles, the EC50 values were 34.9 ± 16.5 mg L
−1
(TOC 0.5 mg L
−1
), 24.8 ± 5.6 mg L
−1
(TOC 2 mg L
−1
), 28.0 ± 10.0 mg L
−1
(TOC 5 mg L
−1
), and 23.2 ± 4.1 mg L
−1
(TOC 10 mg L
−1
). We argue that fate-driven phenomena are often neglected in effect assessments, whilst environmental factors such as the presence of humic acid may significantly influence the toxicity of nanomaterials.