This article analyzes the flows of water and total suspended sediment in different reaches in the lower course of the Negro River, the largest fluvial blackwater system in the world. The area under study is the Anavilhanas Archipelago, which is a complex multichannel reach on the Negro River. Between the years 2016 and 2019, data about water discharge, velocity, and concentration of total suspended solids (TSS) were acquired in sample sections of the Negro River channels located upstream, inside, and downstream of the Anavilhanas Archipelago. In the study area, the Negro River drains an area greater than 700,000 km², and the mean water discharge observed before the Anavilhanas was about 28.655 m³·s⁻¹, of which 97% flows through two channels of the Archipelago close to the right and left banks. The mean TSS concentration of the Negro River upstream and downstream the Archipelago was 3.28 mg·L⁻¹ and 1.63 mg·L⁻¹, respectively. Within the Archipelago, we observed more TSS in the channel on the left bank of the Negro River (mean of 4.50 mg·L⁻¹). The total suspended sediment discharge of the Negro River before (3.14 Mt·year⁻¹) and after (1.43 Mt·year⁻¹) the Anavilhanas Archipelago indicates a 55% retention of the suspended load due to the low water slope and reduced flow velocity caused by the backwater effect of Solimões River on the Negro River. The hydro-sedimentary scenario of the low course of the Negro River characterized in this study indicates a slow and continuous sedimentation process in the Anavilhanas Archipelago. The results presented will serve as a baseline to assess the impacts of the dams on the Branco River, the main tributary for both water and sediment in the Negro River basin.