Abstract Offshore reef systems consist of individual reefs, with spaces in between, which together constitute the reef matrix. This is the first comprehensive, large-scale study, of the influence of an offshore reef system on wave climate and wave transmission. The focus was on the Great Barrier Reef (GBR), Australia, utilizing a 16-yr record of wave height from seven satellite altimeters. Within the GBR matrix, the wave climate is not strongly dependent on reef matrix submergence. This suggests that after initial wave breaking at the seaward edge of the reef matrix, wave energy that penetrates the matrix has little depth modulation. There is no clear evidence to suggest that as reef matrix porosity (ratio of spaces between individual reefs to reef area) decreases, wave attenuation increases. This is because individual reefs cast a wave shadow much larger than the reef itself; thus, a matrix of isolated reefs is remarkably effective at attenuating wave energy. This weak dependence of transmitted wave energy on depth of reef submergence, and reef matrix porosity, is also evident in the lee of the GBR matrix. Here, wave conditions appear to be dependent largely on local wind speed, rather than wave conditions either seaward, or within the reef matrix. This is because the GBR matrix is a very effective wave absorber, irrespective of water depth and reef matrix porosity.