Marine invertebrates are a critical component to understanding how global change is affecting coastal marine environments. This dissertation encompasses two chapters investigating the relationships between marine invertebrates and their microbiomes in the context of pollution. Chapter one focuses on the emerging field of marine invertebrate larval microbiomes. Organisms heavily rely on consortial symbioses with microbes, yet little is known about marine invertebrate microbiomes, especially during early development. Using 16S short-read sequencing, bacterial composition and relative abundances of S. purpuratus gametes, larvae, habitat, and diet was tracked. The results show that the S. purpuratus larval microbiome changes in composition and relative abundance throughout development, with specific bacterial taxa associated with these variations. Notably, the S. purpuratus larval microbiome is unique compared to the microbiota associated with its habitat and diet. Furthermore, vertical transmission of bacterial genus Psychromonas via eggs is likely critical to S. purpuratus embryonic development, and horizontal transmission via sea water habitat is crucial to seeding the feeding S. purpuratus larval microbiome. These results help elucidate what bacterial taxa are important to developing marine invertebrates and how the microbiome is initially seeded. Chapter two investigates marine invertebrate Holobionts in the context of persistent pollutants used by the shipping industry. Organotins (OTCs), specifically TBT, continue to threaten coastal marine environments despite global bans. A literature review and meta-analysis was conducted to investigate the status of OTC pollution and to highlight the ongoing threat posed by TBT and other OTCs to marine invertebrates. The Holobiont is absent from OTC ecotoxicological studies on marine invertebrates, so an experiment investigating how TBT affects the microbiome of early stage S. purpuratus and the microbiota of its diet and habitat was also conducted. Results reveal that OTCs are still freshly input into the marine environment, impact a wide range of marine invertebrate phyla at low concentrations, and are not all regulated or well-studied. Re-prioritization of OTC research is required with a Holobiont-scale approach to address OTC contamination, especially because there are bacterial genera that are capable of OTC resistance and degradation. The experimental results reveal that TBT impacts the microbiota associated with S. purpuratus eggs and sea water, potentially compromising the vertical and horizontal transmission of bacteria important for marine invertebrate development. For effective and ongoing monitoring and management of OTC contamination in marine environments, understanding the effects of OTCs on marine invertebrate Holobionts is critical.