Metal nanoparticles (NPs) are finding ever-wider applications in plant production (agricultural and forestry-related) as fertilisers, pesticides and growth stimulators. This makes it essential to examine their impact on a variety of plants, including trees. In the study detailed here, we investigated the effects of nanoparticles of silver and copper (i.e., AgNPs and CuNPs) on growth, and chlorophyll fluorescence, in the seedlings of Scots pine and pedunculate oak. We also compared the ultrastructure of needles, leaves, shoots and roots of treated and untreated plants, under transmission electron microscopy. Seedlings were grown in containers in a peat substrate, prior to the foliar application of NPs four times in the course of the growing season, at the four concentrations of 0, 5, 25 and 50 ppm. We were able to detect species-specific activity of the two types of NP. Among seedling pines, the impact of both types of NP at the concentrations supplied limited growth slightly. In contrast, no such effect was observed for the oaks grown in the trial. Equally, it was not possible to find ultrastructural changes in stems and roots associated with the applications of NPs. Cell organelles apparently sensitive to the action of both NPs (albeit only at the highest applied concentration of 50 ppm) were chloroplasts. The CuNP-treated oaks contained large plastoglobules, whereas those dosed with AgNP contained large starch granules. The NP-treated pines likewise exhibited large numbers of plastoglobules, while the chloroplasts of NP-treated plants in general presented shapes that changed from lenticular to round. In addition, large osmophilic globules were present in the cytoplasm. Reference to maximum quantum yields from photosystem II (Fv/Fm)—on the basis of chlorophyll a fluorescence measurements—revealed a slight debilitation of oak seedlings following the application of both kinds of NP at higher concentrations. In contrast, in pines, this variable revealed no influence of AgNPs, as well as a favourable effect due to the CuNPs applied at a concentration of 5 ppm. Our research also showed that any toxic impact on pine or oak seedlings due to the NPs was limited and only present with higher concentrations.