Three Scutellaria species (Scutellaria lateriflora, S. costaricana, and S. baicalensis) were grown in different in vitro physical environments: agar, liquid culture, and liquid culture with fiber-supported paper (with initial media volumes of 20 mL and 30 mL). During an 8-week time course, tissue growth was assessed for each species by fresh weight (FW), dry weight (DW), percent DW, and multiplication ratio. Water use and hyperhydricity were also compared. Scutellaria lateriflora plantlets grown in liquid were hyperhydric despite the greatest accumulation of dry mass, but multiplication diminished with time as plants became hyperhydric. In contrast, S. costaricana and S. baicalensis plantlets had higher FW and DW on agar. With all Scutellaria species tested, plantlets grown on agar or fiber-supported paper were not hyperhydric, and fiber-supported paper with 20 mL initial volume yielded plants with the greatest percent DW. The lowered hyperhydricity was related to reduced water uptake. The flavonoids baicalin, baicalein, and wogonin were quantified in plants grown on fiber-supported paper culture. The baicalin concentrations in in vitro cultured S. lateriflora shoots was comparable to those of field-grown plants. The in vitro method presented a unique opportunity to enhance baicalein content and produce wogonin-rich roots. S. costaricana plantlets in vitro showed high levels of the three flavonoids compared with S. baicalensis and S. lateriflora. Growing non-hyperhydric tissues on fiber-supported paper, in vitro, allowed the clonal propagation of Scutellaria species with increased flavonoid content to proceed in a simple, controlled environment.