Trilobites, key components of early Palaeozoic communities, are considered to have been invariably fully marine. Through the integration of ichnological, palaeobiological, and sedimentological datasets within a sequence-stratigraphical framework, we challenge this assumption. Here, we report uncontroversial trace and body fossil evidence of their presence in brackish-water settings. Our approach allows tracking of some trilobite groups foraying into tide-dominated estuaries. These trilobites were tolerant to salinity stress and able to make use of the ecological advantages offered by marginal-marine environments migrating up-estuary, following salt wedges either reflecting amphidromy or as euryhaline marine wanderers. Our data indicate two attempts of landward exploration via brackish water: phase 1 in which the outer portion of estuaries were colonized by olenids (Furongian–early late Tremadocian) and phase 2 involving exploration of the inner to middle estuarine zones by asaphids (Dapingian–Darriwilian). This study indicates that tolerance to salinity stress arose independently among different trilobite groups.