When geological surveys or environmental studies are carried out in brackish water lakes like Lake Nakaumi and Lake Shinji, a sub-bottom profiler (SBP), which images the geological structure of the lake sediment, and sidescan sonar (SSS), which reveals the microtopography of the lake bottom, are essential survey equipment. However, conventional survey equipment was designed for marine operations, and as a result it is large and difficult to use in lakes. A low-cost and compact sidescan sonar and sub-bottom profiler system was developed which can be deployed from a small boat, and easily used in the survey of brackish water lakes. The trade name of the digital sidescan sonar is SportScan (Imagenex Technology Corp., Canada) and the trade name of the sub-bottom profiler is StrataBox (SyQwest Inc., USA). In this paper, we focus on the sidescan sonar. The low-cost sidescan sonar is composed of a towfish connected directly to a power supply (10-16 VDC) and notebook PC through the shipboard towing cable. The operating frequency of the sidescan sonar is 330 kHz, the available operating range is 15m-120m, and the best towing speed is 2-3 knots. A survey of Lake Nakaumi was carried out by combining sidescan sonar/sub-bottom profiler and a DGPS receiver with navigation based on the map software KASHMIR 3 D. This sidescan sonar survey produced a mosaic map of the sediment surface of Lake Nakaumi.