Sargassum meadows play important roles in coastal ecosystems, CO2 fixing, and others. Estimation of their biomass helps conservation of meadows and estimation of the amount of fixed CO2 for blue carbon projects. Most sonars are inefficient in shallow waters because their swaths are limited by water depth. Side scan sonar (SSS) creates a detailed image of the bottom efficiently, even in shallow waters transmitting wide beams. We towed SSS from the ship’s side and scanned the meadow of Sargassum horneri at a small beach in Otsuchi Bay on the Sanriku Coast of Japan during the growing season of 2022. For the truthing, we surveyed with the underwater camera and Single beam echo sounder (SBES) to compare with SSS data. SSS scanned the sea floor of the beach to detect seaweed echoes. The beach consists of a sandy area and a rocky shore. The seaweeds were discriminated from the sand and rocks by their acoustic shadows, and we pinpointed their locations, although the background reflectance strength and pattern were different between the two areas. To estimate the canopy heights, we measured the acoustic shadow lengths of the seaweeds. However, the shadows of the seaweeds, which are located very near to the sonar, are too short to measure. Therefore, we developed a new method to measure their heights from acoustic reflections instead. Our study demonstrated the effectiveness of side scan sonar for mapping Sargassum meadows in shallow waters and estimating their canopy heights with a novel method, which leads to precise biomass estimation.