Abstract Trace fossils are sensitive indicators of environmental fluctuations and, accordingly, ichnological studies have the potential to improve facies characterization of marginal-marine systems. Carboniferous intertidal deposits in eastern Kansas and western Missouri accumulated under contrasting palaeoenvironmental conditions, ranging from the open shoreline to fluvio-estuarine transitions. Comparative analysis of these exposures illustrates lateral variations in trace-fossil content and allows characterization of the intertidal ichnofaunas developed in three sub-environments: open marine, restricted bays and fluvio-estuarine transitions. Openmarine tidal flat ichnofaunas are characterized by (1) high ichnodiversity, (2) marine ichnotaxa produced by both euryhaline and stenohaline forms, (3) the presence of both infaunal and epifaunal traces, (4) the presence of simple and complex structures produced by presumed trophic generalists and specialists respectively, (5) dominance of horizontal trace fossils of the Cruziana ichnofacies, (6) presence of multispecific associations, (7) high density, and (8) wide size range. This ichnofauna is present in heterolithic deposits and reflects the activity of a biota that inhabited tidal flats dominated by normal-marine salinities and connected directly to the open sea. Restricted-bay ichnofaunas display (1) low ichnodiversity, (2) ichnotaxa commonly found in marine environments, but produced by euryhaline organisms, (3) dominance of infaunal traces rather than epifaunal trails, (4) simple structures produced by opportunistic trophic generalists, (5) a combination of vertical and horizontal trace fossils from the Skolithos and Cruziana ichnofacies, (6) the presence of monospecific associations, (7) variable density, and (8) small size. This assemblage occurs in heterolithic facies and records the activity of a brackish-water benthic fauna inhabiting intertidal areas of estuarine basins and embayments. Fluvio-estuarine ichnofaunas are characterized by (1) moderate to relatively high diversity, (2) forms typically present in continental environments, (3) the dominance of surface trails and absence of burrows, (4) temporary structures produced by a mobile deposit-feeding fauna, (5) a mixture of trace fossils belonging to the Scoyenia and Mermia ichnofacies, (6) moderate density of individual ichnotaxa, (7) absence of monospecific suites, and (8) small size. This assemblage occurs in tidal rhythmites and records the activity of a typical freshwater/terrestrial benthos inhabiting tidal flats that were developed in the most proximal zone of the inner estuary under freshwater conditions. Through integration of ichnological and sedimentological data, conventional sedimentological interpretations of marginal-marine depositional systems can be refined and enhanced.