The herbivorous, detrital and microbial pathways are major components of marine food webs. Although it is commonly recognized that these pathways can be linked in several ways, elucidating carbon transfers between or within these pathways remains a challenge. Intertidal flat communities are driven by a wide spectrum of organic matter sources that support these different pathways within the food web. Here we reconstruct carbon pathways using inverse analysis based on mass balancing, stable isotope signatures and tracer data. Data were available on biomass, total carbon production and processing, integrated diet information from stable isotope signatures and the transfer of recently produced carbon through the food web from an isotope tracer study. The integration of these data improved the quality of the inverse food web reconstruction considerably, as demonstrated explicitly by an uncertainty analysis. Deposition of detritus (detrital pathway) from the water column and subsequent assimilation and respiration by bacteria and to a lesser extent by microbenthos (microbial pathway) dominated the food web. Secondary production was dominated by bacteria (600 mg C m−2 d−1), but transfer to higher trophic levels was limited to 9% and most bacterial carbon was recycled back to dissolved organic carbon (DOC) and detritus. Microbenthos secondary production (77 mg C m−2 d−1) was supported by DOC (73%) and detritus (26%) and was entirely transferred up the food web. The higher trophic levels consisting of nematodes, meiobenthos (copepods, ostracods and foraminifera) and macrobenthos fed highly selectively and relied primarily on microphytobenthos and pelagic primary production (herbivorous pathway). Deposit feeding is a common feeding mode among these sediment dwelling fauna, but detritivory was negligible due to this selective feeding. This strong resource selectivity implies that the herbivorous and detrital-microbial pathways function more or less autonomously, with limited interaction.