The nearshore rocky reef environment is an ecosystem of great ecological and economic importance. Rocky reefs are hotspots of biodiversity and many marine food webs around the world rely on primary producers that reside on rocky, or hard-bottom substrate. Along the west coast of North America, the presence of rocky reefs can be considered the first order control for the existence and distribution of marine biota. Like all ecosystems on our planet, rocky reefs face disruptions due to continued changes in the climate over the coming decades. Understanding the response of these ecosystems to climate stressors is crucial for informing management and restoration policies on local, regional, and national scales. Creating an accurate inventory of existing reefs is a crucial first step in quantifying the potential impacts of climate change on these habitats. Advances in remote sensing techniques, specifically airborne LiDAR survey methods provide an opportunity for scientists to quantify nearshore habitats at previously unachievable scales. This paper presents both a methodology for mapping the spatial distribution of rocky reefs, as well as an example of the climate impact assessments that can be conducted once these areas are accurately quantified. The study is therefore divided into two parts. First, a methodology is presented for mapping the extent of rocky reef habitats at high resolutions, using bathymetric measurements from airborne LiDAR surveys. The proposed algorithm extracts roughness values from topo-bathymetric LiDAR data, compares results to existing in situ surveys and classifies substrate as rocky or sandy at 1x1 meter resolution. Second, the effects of different sea level rise (SLR) scenarios on the distribution of rocky reef habitats are explored. After mapping the rocky substrate at two study sites in the San Diego region, a range of SLR scenarios were applied to a depth-stratified ecological model of the local nearshore ecosystems to assess changes in the spatial distribution of key primary producers. This analysis showed a loss in overall habitat area and a shoreward shift in the distribution of rocky nearshore habitats especially in the intertidal zone and in shallow waters populated by surfgrass. The outcomes of this study include both a viable methodology for creating inventories of nearshore rocky reefs at large scales, along with the results of the subsequent SLR assessment. Both avenues of inquiry explored in this study can be expanded upon by future research.