Vision-based underwater robots can be useful in inspecting and exploring confined spaces where traditional sensors and preplanned paths cannot be followed. Sensor noise and situational change can cause significant uncertainty in environmental representation. Thus, this paper explores how to represent mapping inconsistency in vision-based sensing and incorporate depth estimation confidence into the mapping framework. The scene depth and the confidence are estimated using the RAFT-Stereo model and are integrated into a voxel-based mapping framework, Voxblox. Improvements in the existing Voxblox weight calculation and update mechanism are also proposed. Finally, a qualitative analysis of the proposed method is performed in a confined pool and in a pier in the Trondheim fjord. Experiments using an underwater robot demonstrated the change in uncertainty in the visualization.