Monitoring coral reef primary and carbonate production is critical to understand changes in ecosystem function over time and between different reef systems. This is essential with increasing anthropogenic stresses from coastal development, overfishing, pollution, and ocean warming and acidification. However, monitoring these processes at spatial scales relevant to on ground management showing details within individual reefs (100's m 2) and across reef systems (1000's km 2) has been difficult due to lack of biogeochemical models that incorporate physical and biological factors for scaling with remote sensing. There is potential to adopt existing models that use absorbed photosynthetically active radiation (APAR) for estimating productivity, such as the light-use efficiency (LUE) model, which has been successfully applied in terrestrial and open ocean systems. The aim of this thesis was to develop methods for applying the LUE model to coral reef environments with field and remotely sensed data collected at multiple spatial scales. The objectives were to: (1) assess variability in community net productivity and calcification rates for algae dominated reef flats and a seagrass community, (2) assess variability of photosynthetic and calcification efficiencies based on APAR for multiple functional-groups: coral, non-calcareous algae, calcareous algae, sediment, and seagrass, and (3) apply the LUE model to map gross productivity and net calcification using multi-spectral imagery. This thesis focused on two reef systems: Heron Reef, southern Great Barrier Reef and Saipan Lagoon, Commonwealth of the Northern Mariana Islands, which have multi-spectral imagery available for model application. The first chapter of this thesis provided a brief overview of productivity and calcification processes in coral reef systems, and current limitations in monitoring these processes with remote sensing. In Chapter 2 (Obj. 1), field measurements of community net productivity and calcification are reported for algae dominated reef flats and a seagrass community. This study provided the first baseline metabolism and calcification rates for Saipan Lagoon. Both the reef flats and seagrass community had high net productivity that was associated with the dominant presence of algae at all sites. In Chapter 3 (Obj. 2), the theoretical basis for the light-use efficiency model is introduced, and how the model used the relationship between irradiance and photosynthesis to estimate productivity. The relationship between productivity, calcification, absorptance, and irradiance I acknowledge that copyright of all material contained in my thesis resides with the copyright holder(s) of that material. Where appropriate I have obtained copyright permission from the copyright holder to reproduce material in this thesis and have sought permission from coauthors for any jointly authored works included in the thesis.