Two separate forms of application of silver and copper nanoparticles (AgNP and CuNP in a nanocolloidal suspension) to winter oilseed rape seeds were used: (1) seed soaking (S) for 1 h at 20 °C in a NP suspension and (2) additional seed soaking and spraying plants 21-day-old seedlings (SP) with NP. The AgNP and CuNP colloidal suspensions in sterile distilled water were applied in three different NP concentrations (50, 100, 150 mg L−1). However, the changes in the biology and biochemistry of the Brassica napus rhizospheric soil after the application of CuNPs and AgNPs are not considerable, although mostly statistically significant, and the application of CuNPs is more beneficial for this activity than the application of AgNPs. The number of CFUs (colony–forming units) of the tested groups of culturable microorganisms (fungi and copiotrophic, oligotrophic, and siderophore-producing bacteria) indicates the following trend: the abundance of all the tested groups was slightly positively correlated with CuNPs and clearly negatively correlated with AgNPs in each version of application. The soil pH value and tested biochemical soil parameters (IAA: indole-3-acetic acid, PhC: phenolic compounds, FeCC: Fe–chelating compounds) were negatively correlated with AgNPs applied to the seeds (S) at all the tested concentrations and to the seeds and plants (SP) at the concentration of 50 mg L−1. In turn, these parameters were strongly positively correlated with CuNPs applied to the S and SP groups at the concentration of 50 mg L−1 as well as Ag applied to SP at 100 mg L−1. Decrease in dehydrogenase activity (DHA) was lower after the application of CuNPs and AgNPs in S than in the SP way, and the DHA activity was equal to the activity in the control sample after the CuNP application in 100 and 150 mg L−1 concentrations