Net-pen aquaculture results in the introduction of excess fish food an
d fecal matter in coastal waters. These wastes may modify the benthic
environment. Mathematical models are developed in this study to simula
te tidal and wind-driven currents, waves, and the resulting dispersion
of fish food and fecal matter in coastal Maine, a region where limite
d modelling studies have been performed. Cobscook Bay and Toothacher B
ay in Maine are studied in derail through the use of mathematical mode
ls and field data. We find that a systematic, site-specific, step-by-s
tep modeling strategy involving the use of numerical models to simulat
e the overall hydrodynamic environment in combination with a waste-par
ticle transport model can be an extremely powerful method of determini
ng a priori whether aquaculture operations will cause high rates of ne
t-pen waste accumulation at a particular site.