This paper presents an optimization of conditions for microshoot cultures of Nasturtium officinale R. Br. (watercress). Variants of the Murashige and Skoog (MS) medium containing different plant growth regulators (PGRs): cytokinins—BA (6-benzyladenine), 2iP (6-γ,γ-dimethylallylaminopurine), KIN (kinetin), Zea (zeatin), and auxins—IAA (3-indoleacetic acid), IBA (indole-3-butyric acid), 2,4-d (2,4-dichlorophenoxyacetic acid), IPA (indole-3-pyruvic acid), NAA (naphthalene-1-acetic acid), total 27 MS variants, were tested in agar and agitated cultures. Growth cycles were tested for 10, 20, or 30 days in the agar cultures, and 10 or 20 days in the agitated cultures. Glucosinolate and phenolic acid production, total phenolic content and antioxidant potential were evaluated. The total amounts of glucosinolates ranged from 100.23 to 194.77 mg/100 g dry weight of biomass (DW) in agar cultures, and from 78.09 to 182.80 mg/100 g DW in agitated cultures. The total phenolic acid content varied from 15.89 to 237.52 mg/100 g DW for the agar cultures, and from 70.80 to 236.74 mg/100 g DW for the agitated cultures. Extracts of the cultured biomass contained higher total amounts of phenolic acids, lower total amounts of glucosinolates, a higher total phenolic content and similar antioxidant potentials compared to plant material. The analyses performed confirmed for the first time the explicit influence on secondary metabolite production and on the antioxidant potential. The significance was statistically estimated in a complex manner.