Critical to understanding changes to reef community structure in response to anthropogenic impacts is developing effective methods to accurately document the abundance of different reef organisms. The most common techniques used to document coral reef communities rely on two traditional methods based on planar views, which tend to either over- or under-represent canopy-forming organisms, respectively. As canopy-forming organisms are likely to be affected by anthropogenic influences (corals negatively, algae positively), it is essential for monitoring programs to implement methods sufficient to document changes to the vertical dimension of coral reefs. Herein we propose a new survey approach to document canopy effects, suitable for implementation in algal-dominated systems. A vertically stratified transect, modified from a traditional point intercept transect, captures benthic and canopy-forming members of reef communities and estimates three dimensional complexity. To validate the ability of the method to detect changes in vertical reef structure, seaweed was removed from experimental quadrats and monitoring techniques were applied before and after four months of regrowth. A stratified method more accurately captured the three- dimensional change resulting from algal canopy growth, while resolving the over- and under-representation of algal biomass in two other common reef survey methods.