Evolutionary transitions in water column usage have played a major role in shaping ray-finned fish diversity. However, the extent to which vision-associated trait complexity and water column usage is coupled remains unclear. Here we investigate the relationship between depth niche, eye size, and the molecular basis of light detection across the Antarctic notothenioid adaptive radiation. Using a phylogenetic comparative framework, we integrate sequence analyses of opsin tuning sites with data on eye size and depth occupancy from over two decades of NOAA trawl-based surveys. We find a consistent signature of changes in tuning sites suggestive of shifts in their ability to detect lower wavelengths of light. These represent repeated instances of independent tuning site changes across the notothenioid phylogeny that are generally not associated with habitat depth or species eye size. We further reveal an acceleration in the rate of eye size diversification nearly 20 million years after the initial radiation that has manifested in high levels of eye size divergence among closely related taxa. Collectively, our results strongly support a decoupling of the diversification dynamics between opsin tuning sites, eye size and depth, providing a new perspective of the evolution of the visual system in this iconic adaptive radiation.