Beach ecosystems extend from dune to offshore areas along most coasts, and provide essential services that are not provided by any other ecosystem. Indeed, sandy systems contain unique biodiversity and supply nursery and foraging areas for numerous commercially important marine species, such as flatfish. However, these systems are threatened by increasing anthropogenic pressure. Green tides (GT, i.e. accumulations of green opportunistic macroalgae) are a major human-induced threat to marine ecosystems, from inshore to nearshore. This eutrophication process greatly affects both benthic invertebrate communities and flatfish communities, within sheltered and non- or microtidal systems. However, the responses of dynamic open macrotidal sandy systems to eutrophication in the form of macroalgal mats are not yet fully understood. In particular, understanding the effects of GT on two connected biological compartments (infauna and flatfish) within two connected habitats (intertidal and subtidal) is crucial. Here, we set out to assess the influence of several environmental variables, including Ulva biomass, on the variability in infauna and flatfish communities in both the intertidal and the subtidal at four sites impacted or not by GT. In total, 110 biodiversity samples were analysed with classic and novel analytical approaches. Our results demonstrate that the presence of GT specifically impacts intertidal macroinvertebrate communities. However, small effects of GT on subtidal infauna communities, as well as on species-specific flatfish at both intertidal and subtidal, were still detectable. Our findings underline the vulnerability of highly dynamic ecosystems exposed to anthropogenic stress, in particular intertidal sandy shores.