Invasive plant species tend to migrate from their native habitats under favourable climatic conditions; therefore, trophic and other relationships in ecosystems are changing. To investigate the effect of natural organic matter derived from native Alnus glutinosa tree species and from invasive in Lithuania Acer negundo tree species on copper toxicity in Lemna minor, we analysed the dynamics of Cu binding in aqueous leaf litter extracts (LLE) and plant accumulation, morphophysiological parameters, and antioxidative response. The results revealed that A. glutinosa LLE contained polyphenols (49 mg pyrogallol acid equivalent (PAE)/g DM) and tannins (7.5 mg PAE/g DM), while A. negundo LLE contained only polyphenols (23 mg PAE/g DM). The ability of LLE to bind Cu increased rapidly over 1.5–3 h to 61% and 49% of the total Cu concentration (6.0 ± 0.9 mg/L), respectively for A. glutinosa (AG) and A. negundo (AN), then remained relatively stable until 48 h. At the same time, L. minor accumulated 384, 241 or 188 µg Cu/g FW when plants were exposed to Cu (100 µM CuSO4), Cu with 100 mg/L dissolved organic carbon (DOC) from either AG LLE or AN LLE, accordingly. Catalase (CAT) and guaiacol peroxidase (POD) played a dominant role in hydrogen peroxide scavenging when plants were exposed to Cu and 10 or 100 mg/L DOCAG mixtures in both the first (up to 6h) and the second (6–48 h) response phases. Due to functioning of oxidative stress enzymes, the levels of the lipid peroxidation product malondialdehyde (MDA) reduced in concentration-dependent manner, compared to Cu treatment. When combining Cu and DOCAN treatments, the most sensitive enzymes were POD, ascorbate peroxidase and glutathione reductase. Their activities collectively with CAT were sufficient to reduce MDA levels to Cu-induced in the initial, but not the second response phase. These data suggest that leaf litter extracts of different phenolic compositions elicited different antioxidant response profiles resulting in different reductions of Cu stress, thus effecting L. minor frond and root development observed after seven days. The complex data from this study may be useful in modelling the response of the aquatic ecosystem to a changing environment.