1406  2002 Estuarine Research Federation Estuaries Vol. 25, No. 6B, p. 1406–1415 December 2002 Impacts of Hydrological Changes on Phytoplankton Succession in the Swan River, Western Australia TERENCE U. CHAN 1, *, DAVID P. HAMILTON 1, †, BARBARA J. ROBSON 1 ,BEN R. HODGES 2 , and CHRIS DALLIMORE 1 1 Centre for Water Research, University of Western Australia, Crawley WA 6009, Australia 2 Department of Civil Engineering, University of Texas at Austin, Austin, Texas 78712 ABSTRACT: The Swan River estuary, Western Australia, has undergone substantial hydrological modifications since pre-European settlement. Land clearing has increased discharge from some major tributaries roughly 5-fold, while weirs and reservoirs for water supply have mitigated this increase and reduced the duration of discharge to the estuary. Nutrient loads have increased disproportionately with flow and are now approximately 20-times higher than pre-European levels. We explore the individual and collective impacts of these hydrological changes on the Swan River estuary using a coupled hydrodynamic-ecological numerical model. The simulation results indicate that despite increased hydraulic flushing and reduced residence times, increases in nutrient loads are the dominant perturbation, producing increases in the incidence and peak biomass of blooms of both estuarine and freshwater phytoplankton. Changes in salinity associated with altered seasonal freshwater discharge have a limited impact on phytoplankton dynamics. Introduction The ecology and biodiversity of estuarine and coastal waters in many parts of the world are under threat from increasing anthropogenic inputs of nu- trients (Nixon 1995; Cloern 2001). Many of these threats can be attributed directly to expansion of human populations along riparian zones and coast- al catchments (Cooper and Brush 1993). The threats to coastal ecosystems are especially exacer- bated in Australia where 80% of the population lives within 50 km of the coast and the major land drainage basins have undergone large-scale land clearing and hydrological modification since Eu- ropean settlement (Harris 2001). Declining water quality and high rates of sedimentation are the most obvious manifestations of nutrient enrich- ment and land clearing (Zann 1995). Knowledge of the nutrient assimilative capacity of coastal and estuarine ecosystems is essential for management and rehabilitation. Globally, current large-scale efforts to control eutrophication are based largely on the premise that improvements in biodiversity and water quality will be linked directly to reductions in nutrient loads. Such assessments give only rudimentary consideration to response times, hysteresis effects, and hydrological controls, thereby neglecting possible non-linear responses to changes in nutrient loading (Harris 1999). While the major focus of eutrophication man- * Corresponding author; tele: (61 8) 9380 1683; fax: (61 8) 9380 1015; e-mail: chan@cwr.uwa.edu.au. † Current address: Department of Biological Sciences, Uni- versity of Waikato, Hamilton, New Zealand. agement has been on nutrient control strategies, it is also important to consider hydrological mod- ifications that may have an impact on the eutro- phication response. On the Australian continent, weirs and dams have contributed directly to algal blooms by increasing residence times and stratifi- cation of the impounded waters (Sherman et al. 1998) and decreasing flushing of downstream es- tuaries (Davies and Kalish 1994), even though some dredging or estuary opening strategies have improved water quality through increasing flush- ing with marine water (Hearn and Robson 2000; Ranasinghe and Pattiaratchi 2000). The complex- ities of the interactions among freshwater flow and composition, estuary topography and hydrodynam- ics, and human alterations of these features indi- cate that numerical models may be important in quantifying the hydrological responses of estuaries and the resultant changes in water quality. The objective of this study was to develop a quantitative understanding of the way in which the hydrology and water quality of a Western Austra- lian estuary, the Swan River, have been altered by changes in watershed land use patterns and tribu- tary regulation associated with European settle- ment and development. We use a coupled hydro- dynamic-ecological model to make assessments for pre-modification and post-modification cases, with the major focus placed on the likely changes to phytoplankton biomass and species composition. Study Site GENERAL DESCRIPTION The watershed of the Swan River is large (121,000 km 2 ) and dominated by the Avon River