Few studies have characterized disease ecology questions for pathogens with robust environmental stages that cross ecosystem boundaries. In recent decades, terrestrially derived protozoan infections have been increasingly reported in marine mammals. Toxoplasma gondii and Sarcocystis neurona are common pathogens in southern sea otters, but their definitive hosts are terrestrial (felids and opossums, respectively). En route from their terrestrial definitive hosts to a marine animal, parasite stages are subject to diverse environmental forces that determine whether they are effectively mobilized and sufficiently viable to infect a marine host. Intriguingly, we found that the diversity of protozoa genotypes in sea otters, including virulent strains, does not reflect parasite diversity in terrestrial hosts. We hypothesize that (i) environmental forces drive selection of virulent protozoan strains in marine ecosystems; and (ii) virulent parasite strains accumulate and persist in submarine vegetated habitats. Our objectives will generate novel and diverse datasets for an integrative Bayesian modeling approach to test how land-sea environmental forces shape the distribution, population structure and selection of virulent parasites in coastal ecosystems. Objectives are designed to answer two questions: Q1: How do environmental forces across land-sea habitats affect the genetic distribution, transport and survival of T. gondii and S. neurona in the nearshore? And Q2: Are submarine vegetated habitats (kelp and seagrass) hot spots for transmission of virulent pathogens for sea otters? By integrating field, genomics, stable isotope analysis and modeling approaches across land-sea boundaries, this research will provide a new framework to understand how habitat and climate dynamics shape the ecology of virulent pathogens in marine environments. Focusing on kelp and seagrasses has the potential to yield transformative insight on infectious disease transmission in the coastal ocean, with broad implications for diverse host-pathogen systems. Our fully mechanistic model includes numerous ecological processes and incorporates the previously unrecognized importance of submarine vegetation in concentrating pathogens and mediating predator-prey interactions that determine marine host infection patterns. Results will thus represent a fundamental advance in our current understanding of infectious diseases that cross coastal boundaries.