The method of making precise measurements of remote water depth using mmWave technology has great potential for preventing urban waterlogging. To achieve waterlogging prevention, the mmWave system needs to measure the water depth change accurately with a short acquisition time. This paper demonstrates a new accurate mmWave water depth measurement system based on Frequency Modulated Continuous Wave (FMCW) Radar with a center frequency of 77 GHz. To improve distance resolution and lower acquisition time, the Swept Frequency-Cross Correlation (SFCC) algorithm is proposed for the first time to improve the distance computation resolution by 9× and lower time complexity from O(n·logn) to O(n) compared to traditional FFT-based FMCW radar distance computation. A prototype system equipped with a humidity sensor, a processor module and TI’s FMCW radar module is designed for monitoring urban floods in cities. Using the prototype system with the proposed SFCC, the depth measurement error is reduced from 4.5 cm to less than 5 mm, compared to the default radar post-processing algorithm embedded in the radar module.