•The effects of ASTM-dispersed and wastewater-borne AgNPs (NM-300 K) and TiO2NPs (NM-105) were assessed in Daphnia magna.•The behavioural and biochemical responses are distinct after a 96-h exposure to wastewater-borne and ASTM-dispersed NPs.•At the behaviour level, the most pronounced effects on the allocation time are obtained with ASTM-dispersed AgNPs.•At the subcellular level, the wastewater-borne AgNPs are more toxic than wastewater-borne TiO2NPs. Due to their widespread use, silver (Ag) and titanium dioxide (TiO2) nanoparticles (NPs) are commonly discharged into aquatic environments via wastewater treatment plants. The study was aimed to assess the effects of wastewater-borne AgNPs (NM-300 K; 15.5 ± 2.4 nm; 25−125 μg L−1) and TiO2NPs (NM-105; 23.1 ± 6.2 nm; 12.5−100 μg L−1), from a laboratory-scale wastewater treatment plant, on Daphnia magna, at individual and subcellular level. For effect comparison, animals were also exposed to ASTM-dispersed NPs at the same nominal concentrations. The behaviour of D. magna was evaluated through monitoring of swimming height and allocation time for preferred zones after 0 h and 96 h of exposure. Biochemical markers of neurotransmission, anaerobic metabolism, biotransformation, and oxidative stress were subsequently determined. No 96-h EC50 (immobilization ≤ 4 %) could be obtained with wastewater-borne NPs and ASTM-dispersed TiO2NPs, whereas the ASTM-dispersed AgNPs resulted in an immobilization 96-h EC50 of 113.8 μg L−1. However, both wastewater-borne and ASTM-dispersed TiO2NPs, at 12.5 μg L−1, caused immediate (0 h) alterations on the swimming height. Allocation time analyses showed that animals exposed to ASTM-dispersed AgNPs spent more time on the surface and bottom at 0 h, and in the middle and bottom at 96 h. This pattern was not observed with ASTM-dispersed TiO2NPs nor with wastewater-borne AgNPs and wastewater-borne TiO2NPs. At the biochemical level, the more pronounced effects were observed with wastewater-borne AgNPs (e.g. induction of lactate dehydrogenase and glutathione S-transferase activities, and inhibition of catalase activity). This integrative approach showed that: (i) the behavioural and biochemical response-patterns were distinct in D. magna exposed to environmentally relevant concentrations of wastewater-borne and ASTM-dispersed NPs; (ii) the most pronounced effects on allocation time were induced by ASTM-dispersed AgNPs; and (iii) at the subcellular level, wastewater-borne AgNPs were more toxic than wastewater-borne TiO2NPs. This study highlights the need for the assessment of the effects of wastewater-borne NPs under realistic exposure scenarios, since processes in wastewater treatment plants may influence their toxicity.