NaTaO3 has received considerable interest because of its extraordinary photocatalytic water splitting capability and it has been suggested for thermoelectric applications. The ability to synthesize NaTaO3 films is essential for characterization with electrochemical or scanning probe techniques that are difficult to apply to powders. Here we find that with the existing single-step hydrothermal synthesis method for NaTaO3 films, detrimental precursor etching can occur, leading to rapidly disintegrating films. We solved this problem by creating a two-step synthesis. In the first step, a Ta2O5 film is deposited, and in the second step, the Ta2O5 is hydrothermally converted into NaTaO3. With this modification, we systematically obtained durable thin films. When decreasing the synthesis temperature in steps from 393K to 343K, the crystallites gradually change from cubic to more rounded. Hence, the method enables specific control over the surface morphology of the NaTaO3 films. In addition, we show that the samples obtained with the proposed method are sufficiently flat for application of scanning probe microscopy methods.