Inverse analysis was used to model the food webs of two intertidal mudflat ecosystems: Aiguillon Cove (AC) and Brouage Mudflat (BM) (south-western Atlantic coast, France). The aim of the present study is to describe and compare the functioning of these two ecosystems. The method of inverse analysis has been adapted in order to take into account, in a single calculation, two seasons: spring/summer (mid-March to mid-October) and autumn/winter (the rest of the year). Gathering all available data on the two sites, the most important gaps in knowledge were identified with the help of sensitivity analyses: they concerned mainly the exports of material by grazing fish (such as mullet Liza ramada), resuspension of microphytobenthos, and fluxes linked to microfauna which is poorly known for the two systems. The two sites presented the same overall type of functioning (net import of detritus, export of living organic material and higher faunal activity during spring/summer). In both ecosystems, primary production was dominated by the microphytobenthic production, of which a great part was exported via watercolumn advection and biotic vectors (grazing fish), while many secondary producers also used detritus as a food resource. Each system also had its own characteristics, one BM being much more seasonally driven than the other AC. It appeared essential to take the seasons into account, as variations in microphytobenthos production and in meiofauna, macrofauna and biotic vectors led to great differences in the food-web organisation.