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This paper demonstrates the capabilities of a small six element Multi-Angle Swath Bathymetry (MASB) system, deployed in freshwater for the purpose of mapping microbialite structures. It is used to provide both high resolution backscatter imagery, and a bathymetric survey. A 3D sidescan sonar, such as the MASB sonar used in this research, differs from conventional sidescan in that a multiple element receive array is utilized to estimate arrival angles of multiple incoming plane waves. Bathymetry information is calculated using the range of a target and angle of arrival (AOA). The desired signal can be separated from multipath signals which would otherwise corrupt imagery of the bottom. Additionally, a the narrow along track beamwidth and short transmitted pulse length allow for a high resolution image of the lakebed. As the 3D sidescan maintains a small aperture (only slightly larger than sidescan), and uses less channels than multibeam systems (hence fewer electronic components), it is an ideal solution for small platform applications (such as autonomous underwater vehicles AUV) and can be produced less expensively than comparable systems. Surveying can also be performed at a variety of depths (due to multipath elimination), making it possible for a wider range of surveying alternatives such as surface boat mounts (convenient for shallow water), and AUVs. Pavilion Lake, in British Columbia, has been chosen as a survey testbed for two reasons. The primary reason is its importance in analogue space research, having been identified by the Canadian Space Agency as a part of the Canadian Analogue Research Network following the work of , which originally reported unique microbialite structures in Pavilion Lake. The second reason is that Pavilion Lake is acoustically interesting. Both the microbialite formations and the soft sediment regions provide for a wide range of acoustically diverse lakebed with mean backscattered signal levels that vary by more than 30 dB. In ad- dition, the complexity of the many mound structures in the lake, provide a survey scenario that is well suited to test the performance of the MASB system under varied geometries. Surveys included in this paper were performed on several occasions between June 2005 and September 2006. Comparing various visual ground truth results (using techniques such as diver observations, remotely operated vehicles and GPS referenced drop camera observations) with backscatter imagery, the distribution of microbialites, as recorded with MASB sonar was examined. Microbialites are located not only around the lake perimeter walls, but also on the slopes of the mound features within the lake as well as sparse isolated patches within the basins. The sonar images of microbialites taken at Pavilion Lake facilitated the discovery of structures with previously unknown morphologies at depths greater than those previously recorded in . Finally, comparisons are made between MASB sonar and other more conventional systems. It is shown that 3D sidescan can be implemented at low cost in comparison to multibeam systems, and provide an alternative to conventional sidescan in many applications, supplying not only high density imagery, but also co-located bathymetry.