Watermarking is one of the most common techniques used to protect data’s authenticity, integrity, and security. The obfuscation in the frequency domain used in the watermarking method makes the watermarking stronger than the obfuscation in the spatial domain. It occupies an important place in watermarking works in imperceptibility, capacity, and robustness. Finding the optimal location to hide the watermarking is one of the most challenging tasks in these methods and affects the method’s performance. In this article, sample identification information is processed with the method of watermaking on the hiding environment created by using a chaos-based random number generator on biomedical data to provide solutions to problems such as visual attack, identity theft, and information confusion. In order to obtain biomedical data, a lensless digital in-line holographic microscopy (DIHM) setup was designed, and holographic data of human blood and cancer cell lines, which are widely used in the laboratory environment, were obtained. The standard USAF 1951 target was used to evaluate the resolution of our imaging setup. Various QR codes were generated for medical sample identification, and the captured medical data were processed by watermarking it with chaos-based random number generators. A new method using chaos-based discrete wavelet transform (DWT) and singular value decomposition (SVD) has been developed and applied to high-resolution data to eliminate the problem of encrypted data being directly targeted by third-party attacks. The performance of the proposed new watermarking method has been demonstrated by various robustness and invisibility tests. Experimental results showed that the proposed scheme reached an average PSNR value of 564588 dB and SSIM value of 0.9972 against several geometric and destructive attacks, which means that the proposed method does not affect the image quality and also ensures the security of the watermarking information. The results of the proposed method have shown that it can be used efficiently in various fields.