This dissertation explored biological benthic-pelagic coupling in model shallow systems (coastal lagoons) currently at alternative ecological states, most likely the product of intense anthropogenic exploitation of estuarine resources (extractive shellfisheries). Currently, dominant grazers of algae include planktonic microorganisms (nanoflagellates, heterotrophic dinoflagellates, ciliates) instead of significant filtration by macrobenthos. The research focused on the role of benthic suspension-feeding animals in modulating composition, trophic structure, and ecological processes in the planktonic food web at current and hypothetically-increased population densities that would result from restoration.Firstly, laboratory experiments explored the potential of marine mussels (Geukensia demissa, Mytilus edulis) and clams (Mercenaria mercenaria) in grazing and assimilating toxic benthic (Amphidinium carterae) and planktonic (Prorocentrum minimum) dinoflagellates, and another harmful algal species (Aureococcus anophagefferens). Most bivalves tested had the physiological capacity to clear harmful, bloom-producing microalgae. A second stage specifically looked into potential top-down controls exerted by ribbed mussels G. demissa on shallow coastal systems. Microcosm field experiments (0.06 m<super>3</super>) were run with ambient seawater from Long Island bays differing in planktonic biomass and compositional structure. Overall, the results indicated that, when subjected to a mixture of sizes and types of food items, including heterotrophs and toxic algae, the ribbed mussel behaved mostly as a non-selective feeder. When present at high abundances, ribbed mussels might therefore have the potential to improve general water quality.Finally, mesoscale (0.4 m<super>3</super>) field incubations incorporated commercial and non-commercial bivalves (M. mercenaria, G. demissa) and a recently introduced invasive colonial ascidian (Didemnum vexillum) at varying densities, to assess the potential ecological effects of increased benthic suspension-feeding on the current (alternative-state) structure of a coastal lagoon. The response of several planktonic components (picocyanobacteria, picoeukaryotes, auto- and heterotrophic nano- and microplankton, and micrometazoans) was analyzed. In general, the macrobenthic assemblages had interactive effects on the structure (biomass, composition) and functioning (growth rates of primary producers, and growth and grazing rates of nano- and microheterotrophs) of the plankton community.