The variability of coastal carbonate chemistry continues to provide significant hurdles for understanding interactions between anthropogenic and natural CO2 cycling and resultant effects on coastal acidification dynamics. Attribution of the anthropogenic component is vital for identifying the impacts of increasing atmospheric carbon on coastal habitats such as coral reefs, upwelling margins, inland seas, and estuaries. The dynamic nature of these systems has led some to conclude that the baseline shift in atmospheric CO2 is a relatively unimportant driver, but emerging evidence of rapidly acidifying coastal systems suggests otherwise. This dissertation addresses natural and anthropogenic inorganic carbon cycling interactions on diel, seasonal, and decadal time scales to determine current and future acidification trajectories in estuary habitats typical of the northern California Current. Chapter 2 focuses on alterations of diel-scale “carbonate weather” and accelerated rates of acidification in a seagrass habitat resulting from interactions between metabolic CO2 cycling and rising atmospheric CO2 levels. Chapter 3 quantifies how the seasonal variability of carbonate chemistry in two seagrass habitats is altered by rising atmospheric CO2, and how these alterations compare with perturbations driven by altered river discharge, warming temperatures, and eutrophication. Chapter 4 investigates the temporal and spatial dynamics of coastal acidification drivers in a small, open-coast estuary subject to seasonal upwelling and inputs from an agriculturally-developed watershed. This work shows that estuarine habitats are often poorly-buffered against increasing global atmospheric CO2 levels, resulting in accelerated changes of extreme carbonate weather and enhanced CO2 seasonality. Current and future acidification trajectories are significantly modulated by local biophysical processes, including net community metabolism and watershed chemistry. While these local processes control the variance of acidification trajectories amongst estuarine systems, our results suggests the global atmospheric CO2 perturbation is likely the dominant anthropogenic driver of coastal acidification in many systems. Management and policymaking for coastal acidification impacts will be more effective if the spatial and temporal interactions between local and global drivers of acidification are properly accounted for.