The Northwest Power Planning Council (Council) requested the Independent ScientificAdvisory Board (ISAB) to undertake a review of the impacts of estuarine conditions onthe Council’s mission to "protect, mitigate and enhance" fish and wildlife in theColumbia River as affected by development and operation of the hydroelectric system.The ISAB agreed to undertake the review but cautioned that it was unlikely that it couldquantify the impact of changes in the estuary relative to specific program or managementactions taken in the upper river. The ISAB could, however, provide a historicalperspective and qualitative assessment of impacts, identify potentially usefulcollaborations, and provide recommendations concerning future efforts needed to morequantitatively address this issue (letter to Council, Jan. 26, 2000).While conducting this review the ISAB became aware that there was extensive overlapbetween a study by the National Marine Fisheries Service (NMFS) and this ISABassignment. The ISAB expects the NMFS study will add significantly to an informedresponse to the Council. Consequently, this report has been prepared as a preliminaryreply, with additional detail possible following publication of the NMFS study.Before human influence, the Columbia River estuary was a high-energy environmentdominated by physical forces, with extensive sand-beds and highly variable river flows.Several authors have suggested that the biological processes in this environment mayhave been unique on the Pacific coast. The estuary of today, however, has beenextensively modified in terms of physical and biological processes. The developmentand operation of the hydroelectric system have contributed significantly to these changes.Direct effects have been through changes in seasonal flow rates, reduced sedimentdischarge, and resultant changes in the estuary’s energy balance.There is extensive documentation about changes in the estuary over the past century.The major changes resulting from development of peripheral wetlands and their isolationfrom the estuary, development and deepening of the Federal Navigation Channel, andregulation of upper Columbia River flows for hydrosystem needs and flood control. Theeffects of these changes do not function discretely. The estuary is a complex interactionof physical features (predominated by the energy balance between river flow and tidalforces), resultant changes in circulation, salinity intrusion, sediment processes, andultimately the biological consequences of these changes. Superimposed on this dynamicenvironment have been changes in water quality, introduction of exotic species, and theenormous investment in hatchery production of salmonids to mitigate for related lossesdue to the hydrosystem.The question of the potential biological impacts associated with these changes is morecomplicated than detecting the physical impacts. Changes in the biological processesvaried from a fundamental alteration in the basis of the food web to the exclusion of subyearlingchinook and chum salmon from a large portion of the tidal marshes. The effectsof these specific changes, however, are difficult to partition from the effects of numerousother impacts in the Basin. Furthermore, our ability to assess impacts of estuarine conditions on the Fish and Wildlife Program has been limited by a lack of appropriateand available data. Information necessary to meet the 1994 Program objectives wassimply not acquired for the estuary. Similar obstacles were expressed to the ISAB by theNMFS study team who noted that the data are insufficient to even determine the extent ofmodern estuarine use by salmonids.While the ISAB recognizes the limitations of data to directly assess impacts of changes inthe estuary on the Fish and Wildlife Program, after our review it is our assessment thatthese changes have been detrimental to salmonids and the rebuilding objectives of theProgram. We base this advice principally on three major issues:1. The significant loss of peripheral wetlands and tidal channels; these habitats areimportant to the early rearing, survival and growth of chum salmon, sub-yearlingchinook, and smaller coho salmon in other west coast estuaries.2. The extent of change to seasonal flows following development of the hydrosystem.The affects of these changes are closely associated with the impact of thedevelopment of the navigation channel. In combination these developments haveresulted in changes to estuarine circulation, deposition of sediments, and biologicalprocesses.3. The need for precautionary advice given the current state of most salmonidpopulations in the Basin, the magnitude of change in the estuary, and the lack ofinvestigations upon which to base alternative advice.As the 2000 Fish and Wildlife Program is developed, the ISAB recommends anaggressive experimental program targeted to reduce the likelihood of prolongeduncertainty about the impact of estuarine conditions. Such a program should incorporatemonitoring of the physical environment (such as currently begun via the CORIEprogram, Oregon Graduate Institute) combined with evaluation of large-scalemanipulations of estuarine habitats. The intent of these manipulations would be to studychanges presumed to have had negative impacts and to conduct these at a scale that canbe measured within the natural environment. These types of programs would beconsistent with the vision statement in the 2000 Fish and Wildlife Program:"Wherever feasible, this program will be accomplished by protecting and restoring thenatural ecological functions, habitats, and biological diversity of the Columbia RiverBasin."The types of large-scale programs that are envisioned include:a) removal of dykes in the lower river and upper estuary to restore connectionsbetween peripheral floodplains and the river or fluvial zone of the estuary;b) actively managing sources of salmonid predation in the estuary through restorationof natural habitats, removal of habitats artificially created due to channel constructionand/or maintenance, or controlling predator populations.c) establish an allocation of water within the annual water budget for the Basin, thatwould simulate peak seasonal discharge, increase the variability of flows duringperiods of salmonid emigration, and restore tidal channel complexity in the estuary(aided by removing pile dykes where feasible).