A complex variety of marginal-marine microtidal environments from Kouchibouguac Bay, New Brunswick, Canada, present an opportunity to ichnologically and sedimentologically characterize microtidal settings in a high-latitude, temperate subarctic climate. Variations in bioturbate fabrics and distribution of infauna, analysis of the distributions of sediments and physical sedimentary structures, and the distribution of total organic carbon (TOC) can be associated with characteristic depositional processes. From these data typical sedimentary facies associations are produced. In outer estuary tidal inlets and areas of the flood-tidal deltas, strong currents and wave action eradicate the ichnological signature, resulting in variably laminated and bedded sand. In the central estuary, infauna activity coupled with generally low hydraulic energy levels lead to an absence of primary sedimentary structures. The inner estuary near bay-head deltas experiences riverine currents and freshwater influence. As a consequence, primary sedimentary structures are preserved. Mapping of infauna, sediment texture, TOC, and salinity reveals strong links between animal distribution and these three physicochemical parameters. Consequently, the distribution and type of bioturbation observed is at least passively related to grain size, TOC, and salinity. In outer estuaries and lower-central estuaries, salinity is near marine levels and fluctuates minimally. The distribution of infauna in these areas corresponds directly to sediment texture and TOC. Further up the estuaries, lower and fluctuating salinities—in addition to sediment texture and TOC content—control the distribution and diversity of infauna. Mapping of diversity and infaunal size up-estuary reveals two significant trends attributable to salinity stresses: (1) vermiform diminution, and (2) a significant decrease in infaunal diversity.