Previous documentation has proposed tectonic activity from the Neogene to Holocene as one important control on drainage development in the Amazonian lowland. However, recording tectonic structures in this region has been challenging due to environmental difficulties, including the low topography and dense vegetation cover that do not favor natural exposures. For this reason, the role of tectonics in determining river dynamics, morphology, and sediment deposition in Amazonia has been suggested with caution. Despite limitations, morphostructural lineaments have provided useful information to support fault reactivation in several areas of the Amazonian lowland. However, further documentation is required to map the faults and describe their geometry. This approach is essential to better understand the geotectonic model of this region. In this work, analyses of high-resolution optical imagery of three Amazonian shallow water lakes provided exceptional views of an abundance of linear features on the beds of these lakes. Although based on indirect evidence from remote sensing data, the quality of the images allowed the geometry of these underwater features to be characterized in detail. The most striking are sets of NE–SW lineaments that frequently intercept NW–SE trending lineaments with offsets of up to 500 m in the horizontal plane. These characteristics support dextral faults with strike–slip rates in the study areas. The faults display trends compatible with the geotectonic model proposed for the Brazilian Amazonia region. They also control the morphology of lakes and rivers, as indicated by the parallelism and/or continuity into straight lineaments that define lake margins and river courses, including the courses of large rivers, such as the Solimões and Amazonas Rivers. Available radiocarbon ages of deposits from the lake bed sediments and from related floodplain deposits are consistent with the proposal of faulting during the latest Holocene, even only a few hundred years ago.