Despite the significant progress made in ecotoxicological research on nanoparticles (NPs), there is still very limited information available regarding the biological effects of certain types of NPs such as Co3O4 and Mn2O3. Only a couple of studies provide data on their impact on aquatic organisms whereas, alarmingly, these NPs have been proposed to have high toxicity potential. In addition, more data are needed to determine whether the adverse effects the metal NPs induce on aquatic organisms are rather due to their chemical or particulate nature. To address these open questions, the (sub)lethal effects of Co and Mn NPs in parallel with the respective soluble metal salts on Daphnia magna were studied. The aims of the current study were to i) assess the acute toxicity of Co3O4 and Mn2O3 NPs (primary size 10–30 nm) to D. magna, ii) evaluate whether the acute NP exposure at sublethal concentrations influences D. magna post-exposure feeding behaviour and iii) quantify D. magna metal body burden after exposure and after the post-exposure feeding to estimate the potential of trophic transfer of metals. Flow cytometry and total reflection X-ray fluorescence spectroscopy were applied for feeding and metal body burden evaluations, respectively. CuO NPs (primary size 22–25 nm) that are very toxic to D. magna were included in the study as a positive control. Since the release of metal ions is an important possibility for toxicity of metal NPs, soluble Co-, Mn- and Cu-salts were analysed in parallel. The solubilisation of Co3O4 NPs in the OECD202 assay conditions was 0.1% and Mn2O3 NPs 35%. Mn2O3 NPs also produced reactive oxygen species in abiotic conditions. However Co3O4 and Mn2O3 NPs were not acutely toxic to D. magna (48 h EC50 > 100 mg metal/L) at OECD202 assay conditions. The 48 h EC50 values of soluble Co- and Mn-salts were 3.2 mg Co/L and 41 mg Mn/L, respectively. Post-exposure feeding behaviour after 48 h exposure to sublethal concentrations (≤10 mg/L) of Co3O4 and Mn2O3 NPs differed from that of the unexposed (control) D. magna only at the highest exposure concentrations but was comparable to the feeding behaviour of the respective metal salt-exposed organisms. Upon 48 h exposure, dose-dependent increase of D. magna total metal body burden in case of both the NPs and the soluble salts was observed. After 48 h post-exposure feeding with algae C. reinhardtii (depuration): D. magna body burden remained elevated (up to 760-fold compared to the control organism) only in case of the NPs. This may indicate potential for trophic transfer of NPs/heavy metals and thus hazard for freshwater ecosystem.