A major challenge in environmental monitoring is differentiating of true impacts from changes due to natural variation or cycles in ecosystem function. In our study the use of the BACI sampling design has allowed for discrimination of construction impact from natural variation. Impacts have been detected in salinity, sediment accretion, D.O., phosphorus concentration, macrophyte community composition, algal productivity as well as macroinvertebrates and fish. These changes are likely the result of construction of the highway bypass of Jacksonville , NC . It is impossible to say whether these impacts will prove to be short-term or persist beyond the completion of the highway since data collection after construction was discontinued due to a lack of funding. It appears the impacts resulting from construction phase increased rates of runoff from the watershed due to road clearing, impeded fluxes of water from floods and importantly tides due to the presence of temporary culverts at the site. Changes in soil surface elevation due to sediment displacement during road fill placement, and increased sediment flux from road fill and clearing also occurred. These impacts should be temporary, and the system may return to its normal state after several growing seasons, provided sediment and nutrient changes do not remain altered. Of concern, however, is the impact of reduced salinity on the long-term biota of Wilson Creek . Unfortunately, the study has not been continued so it is impossible at this stage to assess the recovery of the site and determine if the biota have returned to conditions near the reference conditions. Fortunately, the design of the study will allow for a follow up study to assess recovery.