Worldwide, the escalation of nutrient pollution from multiple sources is causing the collapse of coastal marine ecosystems. Anthropogenic inputs of nitrogen (N) from agriculture, fossil fuel and biomass burning, and urban development have ushered in an era of coastal eutrophication and consequently, widespread loss of biodiversity and ecosystem services. Often cited as the “canaries” of the sea, corals and the reefs they form are highly sensitive to this pollution, and the dramatic loss of coral reef habitat has coincided with human development. Yet, as this problem has only received attention in the last several decades, there is a critical need to understand how humanderived sources of pollution have changed since industrialization, and establish historical baselines, from which we can assess global change in today’s world. This dissertation expands on our understanding of coastal pollution using isotope ratios of common tropical benthic biota. In chapter 1, I show that gorgonian corals are particularly useful recorders for environmental N sources, and report several considerations for sampling and data interpretation using in situ collections and lab experiments. In chapter 2, I use common benthic calcareous algae to quantify spatial and intra-annual variability in the Florida Keys. Using a comprehensive water quality dataset I found no evidence to suggest that isotope ratios are impacted by long-term water quality parameters. Chapter 3 discusses an applied use of these methods to assess sewage N pollution to reefs along the Mexican Yucatan peninsula. I show that in developed areas, N isotope ratios are among the highest reported for corals, and these values are correlated with the presence of enteric bacteria. Finally, chapter 4 utilizes a museum collection of gorgonians to reveal long-term trends in C and N isotope ratios across the Wider Caribbean since the mid- 1800s. Changes in these values over time suggest that the 13C Suess effect, and the explosive use of agricultural fertilizers since the 1960s are detectable in these octocorals.