Ultraviolet-visible absorption spectroscopy is widely used to monitor water quality, and rapid optical signal detection is a key technology in the process of spectrum measurement. In this paper, an ultrafast spectrophotometer system that can achieve spectrum data acquisition in a single flash of the xenon lamp (within 200 ns) is introduced, and a real-time denoising method for the spectrum is implemented on a field programmable gate array (FPGA) to work cooperatively with the nanosecond spectrum acquisition system, in order to guarantee the quality of the spectrum signals without losing running speed. The hardware of the data acquisition and processing system are constructed on a Xilinx Spartan 6 FPGA chip and its peripheral circuit, including an analog to digital converter and a complementary metal-oxide-semiconductor transistor (CMOS) sensor’s diver circuit. An oversampling method that is suitable for the CMOS sensor’s output is proposed, which works on the CMOS sensor’s dark current noise and readout noise. Another moving-average filter method is designed adaptively, which works on the low-frequency component to filter out the residual spectrum noise of the spectrum signal. The implementation of the filter on the FPGA has been optimized by using a pipelined structure and dual high-speed random-access memory (RAM). As a result, the CMOS linear image sensor successfully captured the spectrum of xenon flash light at the readout clock frequency of 500 kHz and the processing manipulation to the full UV-Vis spectrum data was accomplished at a sub-microsecond speed performance. After the digital filter and oversampling technology were implemented, the coefficient of variation of the measurements reduced from 9.57% to 1.74%, while the signal noise ratio (SNR) of the absorption spectrum increased nine times, compared to the raw data of the CMOS sensor’s output. The tests towards different analyte samples were conducted, and the system shows good performance on distinguishing different concentrations of different analyte solutions on both ultra-violet and visible spectrum bands. The present work showcases the potential of the CMOS sensor’s technique for the fast detection of contaminated water containing nitrate and organic compounds.