Disease transmission in sessile filter feeders is proposed to occur by freely drifting infectious particles (IP) released by sick and dead animals. A susceptible /infected/particle (SIP) model is developed to analyze disease processes. The infection Ro, estimated from the proposed model, increases in proportion to the ratio of particle production to removal processes. An infective dose sub-model assumes that exponentially declining numbers of susceptibles occur with increased body burden. Susceptibles with the highest body burden become sick at any time. This SIP model is incorporated into a coastal circulation model (ROMS) to investigate the transport and dilution effect of circulation in a generic shallow estuary. Populations of susceptible animals are distributed in the estuary to show that susceptible populations with one infected animal becomes infected in a few days. The rate of spread of an infection between separated populations depends on the distribution and separation of these populations along with the details of the estuary geometry and circulation.