Methane (CH₄) accumulates in bottom waters of lakes, however, the extent and drivers of inter-lake variation in bottom-water CH₄ concentrations are poorly understood and have been studied mainly in northern lakes. This limits predictions of how bottom-water CH₄ concentrations respond to warming and eutrophication in lakes, and how these changes might influence surface-water CH₄ concentrations and, consequently, CH₄ emissions. We report 168 measurements of paired bottom- and surface-water CH₄ concentrations from 46 African lakes spanning a wide range of surface area (SA; 0.02–67,075 km²) and maximum depth (2–180 m). Bottom-water CH₄ concentrations ranged from 7 to 5,608,382 nmol L⁻¹, spanning six orders of magnitude, and increased with increasing stratification, quantified from vertical density profiles using potential energy anomaly (PEA) and mixed layer depth (MLD), and inferred from NH₄⁺ concentrations or vertical conductivity gradients. Surface-water CH₄ concentrations ranged from 7 to 168,114 nmol L⁻¹ and increased with both bottom-water CH₄ concentrations and vertical stratification (positively related to PEA and negatively to MLD). The most strongly stratified lakes exhibited high bottom-water CH₄ concentrations, resulting in enhanced vertical transfer of CH₄ to surface waters despite lower vertical diffusion coefficients. In addition, these lakes had shallower mixed layers and therefore thinner oxygenated surface layers, likely reducing CH₄ removal via methane oxidation. The positive relationship between both bottom- and surface-water CH₄ concentrations and chlorophyll-a (Chl-a) has previously been interpreted as reflecting enhanced methanogenesis driven by phytoplankton-derived organic matter delivered to sediments. However, such relationships may be indirect and should be interpreted cautiously, as Chl-a was negatively related to MLD in our dataset, and both bottom- and surface-water CH₄ concentrations were also negatively related to MLD. The ratio of surface to bottom CH₄ concentrations (surface:bottom CH₄ ratio) may indicate the relative increase in surface CH₄ in response to increases in bottom CH₄ driven by warming and eutrophication. This ratio was negatively related to bottom depth, PEA, and MLD, and positively related to bottom-water O₂, indicating that the relative increase in surface-water CH₄ with increasing bottom-water CH₄ is greater in shallower, less stratified systems than in deeper, more stratified systems. Diffusive CH₄ emission rates were highest in shallower, less stratified systems, where the response of surface-water CH₄ to increases in bottom-water CH₄ is expected to be greatest, as indicated by high surface:bottom CH₄ ratios. We further tested whether surface-water CH₄ concentrations scale with simple metrics in a dataset including highly stratified, small, and deep crater lakes with elevated hypolimnetic CH₄. A multiple linear regression using SA and Chl-a explained ~51 % of the variance and appears suitable for upscaling dissolved CH₄ concentrations. This approach could enable large-scale extrapolation of diffusive CH₄ emissions using spatial datasets for SA and remotely sensed Chl-a.