Roberts Bank, part of the Fraser River delta system on Canada’s Pacific coast, is a dynamic estuarine environment supporting important fisheries as well as internationally significant populations of migratory shorebirds. The 8000ha bank environment comprises a complex of riparian boundaries, intertidal marshes, mud and sand flats, eelgrass meadows, macroalgae and biofilms. Anthropogenic developments (a ferry causeway in 1961 and a port causeway in 1969) have been responsible for changes in tidal flow patterns, tidal elevation, sediment transport and the net expansion of eelgrass beds. The goals of the present study were to (1) directly compare geotechnical properties spanning each side of the coalport causeway, and (2) enhance our understanding of the intercauseway ecosystem under a high-resolution sampling design. Sediment properties (grain size, porosity, organic content, and chlorophyll) and biological communities (eelgrass, macrofauna (0.5–1.0mm) and meiofauna (0.063–0.5mm)) were surveyed in 1997 at three stations outside the intercauseway area and three lateral transects spanning the intercauseway tidal flat at tidal heights representing three different habitats: biofilm, Zostera japonica, and Zostera marina. A fine-silt organic-rich porous deposit was observed on the shoreward north side of the coalport causeway relative to the south counterpart, suggesting that consolidation and erosion processes could likely not keep pace with the deposition of Fraser River silt. High chlorophyll levels were found in the protected shoreward northern border of the ferry causeway where fine sands dominate and higher water transparency exists, owing to the redirection of the silt-laden river plume by the coalport causeway. Principle Components Analysis revealed a positive relationship between these porous, organic-rich sediments and cumacean abundance in all regions where eelgrass was absent, including the north side of the coalport causeway. Further, a positive relationship was found between biofilm components (chlorophyll and silt), polydora, and harpacticoid copepod abundance, which, together with cumaceans, are food for Western Sandpipers, Calidris mauri. Finally, 52% of the intercauseway variation was explained by direct correlations between eelgrass attributes and fauna consisting of bivalves, caprellids, and harpacticoid copepods (root biomass, leaf area index), the latter being prey for juvenile salmon which depend on eelgrass beds as rearing habitat. These habitats are vulnerable to changes in tidal flow patterns, tidal elevation, sediment transport, and water clarity that could be caused by future port development and/or sea level rise in response to climate change.