Sediment concentration of rivers in developing countries has been increasing greatly over the last 50 years due to the conversion of forest to continuously cultivated land with the increasing population. Few studies have addressed its effect on sedimentation and water quality of the lakes by analyzing bottom sediment characteristics. In this study, the objective was to investigate the spatial distribution (and their interrelationships) of the bottom sediment characteristics in the largest lake in Ethiopia, Lake Tana where water hyacinths have been spreading rapidly during the last decade. Sediment samples were collected from the lake bottom at 60 locations and analyzed for texture, organic matter, total nitrogen, and available phosphorus. Bottom sediment samples had a median of 75% clay, 13% silt, and 9% sand. Clay was greatest in the northwestern part and smallest in the areas near the major rivers entering or exiting the lake. Clay percentage and lake depth were strongly correlated. The mean organic matter content of bottom sediment was 16 g kg−1, total nitrogen 0.8 g kg−1, and Olsen available phosphorus 19 mg kg−1. Phosphorus concentrations peaked where water hyacinths were found in the northeastern part of the lake. This study will serve as a baseline for future water quality and sedimentation changes in Lake Tana. In particular, it might aid in explaining the spread of the water hyacinths.