The Penghu archipelago comprises 64 basaltic volcanic isles lying on the Taiwan Strait between mainland China and Taiwan. The water around and within these isles is shallow and poses considerable difficulty in echo sounding detection for bathymetry. Most existing bathymetry data around such areas are in water depths of greater than 5 m. Therefore, when the water depth is less than 5 m the data tend to be over-extrapolated. In this study, a remote sensing method provides a more effective approach to recording shallow water depths compared to traditional soundings using multitemporal images collected by optical/near-infrared sensors from SPOT satellites. This method employs optical energy reflections to obtain the water depth. In this study, we made several improvements wherein a relative atmosphere correction technique was used to calibrate two images within a similar atmospheric condition. We then compared the satellite images acquired from different dates to obtain the local water attenuation coefficient of sunlight. Finally, we developed a means to estimate the water attenuation coefficient and bottom reflectance which will satisfy the two parameters across the study area. Our results show a high-resolution map of shallow bathymetry for the Penghu archipelago and revealed a maximum depth of about 20 m. This study provides an efficient approach for shallow bathymetry retrieval. Many detailed features revealed by this approach may contribute to further geological research and developments in harbour and coastal engineering.