The flow of organic matter along the main navigation channel of Ria Formosa, Portugal, was assessed using determinations of suspended particulate matter (SPM), particulate organic matter (POM), and chlorophyll a (chla) concentrations in conjunction with stable isotope values of primary producers, particulate matter, and two filter feeders. SPM in the lagoon is dominated by inorganic particles comprising 80% of total weight with organic matter averaging about 20%. The algal component of the POM averaged about 5% with the remainder comprised of detritus. The δ13C values of primary producers ranged from −9.1‰ in the intertidal seagrassZostera noltii to −30.7‰ in the red seaweedBostrychia scorpioides revealing underlying differences in the mechanisms of carbon uptake. The δ13C value ofB. scorpioides, which develops entangled on the salt marsh speciesSpartina maritima, suggests that its main source of inorganic carbon is atmospheric CO2. The δ13C values of the high marsh macrophyteSarcocornia perennis significantly increased with distance from the ocean while δ13C values ofZ. noltii decreased, probably because higher decomposition of organic matter at inner stations lowers the δ13CO2 value in the water. The δ15N values of Ulvales, seagrasses, and marsh plants significantly increased from outer stations to inner stations. This increase may be due either to recycling of nitrogen (N) within the marsh (with loss of light N2 or NH4) or to inputs of isotopically heavy N from sewage. The δ15N values of particulate matter showed an opposite trend, which indicates higher microbial degradation of organic matter at the inner lagoon. The data demonstrate that the seston in the lagoon is a mixture of detritus from lagoon primary producers with a minor contribution of microalgae. The filter feeders are most likely assimilating a mixture of phytoplankton and microphytobenthos. Digestion of lagoon seston is selective. The δ15N values of both muscle and digestive gland of filter feeders showed the opposite gradient of particulate matter indicating that the depleted δ15N of SPM at inner stations was not assimilated or even ingested. Stable isotopes values did not differ between the filter-feeders—the musselMytilus galloprovincialis collected on buoys and the clamTapes decussatus collected in the sediment—suggesting a considerable mixture of benthic-pelagic organic matter throughout the water column. Assessment of the changes in isotopic decomposition of detritus as it decays is required to refine our understanding of organic matter transfers in detrital food webs.