BaTiO3, SrTiO3, and BaxSr1−x TiO3 thin films, as well as multilayers in the SrTiO3-BaTiO3 system, have been prepared on Ti substrates in newly constructed flow-system equipment by the hydrothermal-electrochemical method. The synthesis parameters (temperature of 120–200 °C, flow rate of 1–50 cm3/min) allow fabrication of dense, single-phase films with different morphology by controlling nucleation and/or growth rates. The flow system enables also an easy fabrication of SrTiO3/BaTiO3 and BaTiO3/SrTiO3 multilayers with variable chemical composition and microstructure across the film thickness. The multilayers can be prepared in only one experiment by simply changing the kind of flowing solution and/or adjusting the processing conditions.