preprint – 1 of 7

The Effects of Freshwater Flows and Salinity on Phytoplankton Biomass and Composition in an Urban Estuary, The Swan River,

D. P. Hamilton, T. U. Chan, B. J. Robson and B. R. Hodges1 Centre for Water Research, The University of Western Australia, Nedlands, WA 6907, Australia

ABSTRACT Estuarine residence times regulate not only biomass, but also phytoplankton succession. In the Swan River estuary, Western Australia, dinoflagellate and marine diatoms tend to dominate during periods of low flow and high residence times, whereas the faster-growing freshwater diatoms and chlorophytes are associated with higher flow rates. Modifications to the estuary and its catchment area over the last century have considerably reduced residence times and may favour dinoflagellate and marine diatom dominated populations. Anecdotal evidence also suggests a greater regularity of summer blooms dominated by these groups in recent years.

INTRODUCTION A number of factors make estuaries particularly vulnerable to and algal blooms. First, human populations tend to proliferate around estuary margins, often leading to increases in land disturbance and nutrient inputs (Boynton et al., 1992). For example, Australia's geographic demography is associated with high concentrations of population along coastal land margins relative to inland areas and the arid interior in particular.

Estuaries are sometimes considered to be the terminal repository for much of the sediment and nutrients derived from terrestrial sources via tributary inflows. They may therefore act to filter sediments and nutrients from inputs to adjoining coastal systems, provided that processes of burial and immobilisation of nutrients are maintained (Fisher et al., 1988). However, density stratification of freshwater and marine water leading to salt wedge formation, a phenomenon associated particularly with estuaries (Geyer, 1989), may lead to oxygen depletion in bottom waters, and subsequent remobilisation of sediment nutrients through reduction processes (Ackroyd et al., 1987). Also, resuspension of bottom material through wind or tidal action may increase water column concentrations of sediments and nutrients (e.g. Mortimer et al., 1998).

Well documented cases of stability of buoyancy fronts in the salt wedge region of estuaries, and associated zones of stagnation, may allow sufficient time for net phytoplankton growth to occur before cells are transported seaward and out of the system (Malone et al., 1988; Cloern, 1996). Thus the coalescence of a number of favourable physical and chemical changes in the water column (e.g. light, temperature and nutrients), that allow phytoplankton to grow at near maximal rates, together with sufficient hydraulic residence time in the estuary, will determine whether phytoplankton blooms may occur. However, what is often not fully appreciated is the capacity of estuary residence time to regulate not only the eventual biomass, but also the succession of phytoplankton species. When residence times are of the order of cell doubling times or less, phytoplankton species or taxa that out-compete others by virtue of higher growth rates will be favoured. . This effect works in conjunction with the more readily identifiable pattern of phytoplankton succession in estuaries that is associated with salinity gradients, leading to succession amongst freshwater, brackish and marine adapted species (Thompson, 1998).

1 Presently at the Dept of Civil Engineering, University of Texas at Austin, USA.

To appear in Proceedings, 3rd International Hydrology and Water Resources Symposium (Hydro 2000), Vol 1, pp. 114- 119, 2000. preprint – 2 of 7

In this paper we examine the relationship of phytoplankton biomass and species composition to tributary inflows and salinity in a Western Australian estuary, the Swan River. We also speculate on how human modifications to the flow regime in the Swan River may have impacted upon bloom frequency, duration and composition of the dominant taxa.

STUDY SITE

The Swan River estuary is fed by a large catchment (area = 120,000 km2) that is dominated by the Avon River (catchment area = 119,500 km2). Rainfall varies over the catchment from ~ 900 mm yr-1 in coastal regions to ~ 300 mm yr-1 around the eastern boundary, while respective water runoff of these locations per 100 mm of rainfall may be > 70 mm and < 5mm (Viney and Sivapalan, in press). The climate can be classified as Mediterranean, with typically 70% of rainfall confined to the winter and spring months of June to September. Correspondingly, tributary runoff is highly seasonal, with little or no flow occurring in the first 4-5 months of each year in the Avon River. Smaller tributaries, most of which enter on the , are also highly seasonal, although flow may vary from seasonal (e.g. ) to perennial in the case of some urban drains (Donohue et al., in press). Groundwater inflows, which are mostly associated with sandy soils of the Swan Coastal Plain, vary little seasonally but may contribute up to 10% of freshwater inputs to the estuary in summer and autumn months when flows from surface-fed tributaries are small (Linderfelt and Turner, in press).

In summer and autumn, water of marine origin intrudes along the Swan Coastal Plain up the Swan River to approximately 50 km upstream of the estuary mouth at Fremantle (Fig. 1). Winter runoff drives the salt wedge seaward, occasionally close to Fremantle in very wet years (Stephens and Imberger, 1996). Tidal excursions of the salt wedge are typically of the order of 1-3 km although synoptic forcing may displace the salt wedge by around 10 km, corresponding to the duration of passage of low- and high-barometric pressure systems (Hamilton et al. in press).

N Ellen Brook Agriculture (1950s-) city Urbanisation (1990s-) Urbanisation Indian Avon River Ocean Clearing, salinisation Fremantle Swan River (1900s-) Channel River training (1958-71) Dredging ~2m to ~14m (1892-) Ascot Waters Boat harbours Mundaring and marinas (1990s-) Weir (1902) 1 0 1 2 km Kent Street Weir (1920s) (1940)

Figure 1. Map of the Swan River showing major tributaries, estuary mouth, and (in italics) some of the major changes that have had an impact on the estuary hydrology, and the year(s) that the changes occurred. Note the narrow constriction between Canning River and Perth city, which delineates the lower basin towards Fremantle from the upper basin.

To appear in Proceedings, 3rd International Hydrology and Water Resources Symposium (Hydro 2000), Vol 1, pp. 114- 119, 2000. preprint – 3 of 7

The highly seasonal hydrology of the Swan River estuary is reflected in a well documented succession of phytoplankton taxa (John, 1994; Thompson and Hosja, 1996). The high flow period of winter and early spring is dominated by freshwater diatoms, which are typically succeeded by a short-lived bloom of freshwater chlorophytes. In summer and autumn, estuarine and marine assemblages are dominant and typically show transitions between dinoflagellates (e.g. Gymnodinium spp. and Prorocentrum spp.) and the cosmopolitan coastal diatom Skeletonema costatum. Blooms of dinoflagellates (Hamilton et al., 1999) and more recently (February, 2000) the blue-green alga Microcystis aeruginosa (Hamilton, 2000) are of particular concern in terms of biodiversity, amenity and long-term impacts on the estuary ecosystem.

The hydrology of the Swan River has undergone substantial modifications in the past century (see Fig. 1), and it is likely that these changes have also affected phytoplankton succession. Extensive dredging of the estuary occurred at Fremantle, commencing in 1892, to allow passage of larger boats upriver. The channel entrance at Fremantle has thus been altered from < 2m to ~ 14m, and the main basin below the Narrows (see Fig. 1) is now predominantly marine (Hodgkin and Hesp, 1998). A succession of dams, notably Canning Dam and , were constructed for water supply through the 1900s. In their original state these tributaries (i.e. Canning River and Helena River) were unlikely to have exerted a major influence on winter flows, due to the dominance of the Avon River. However, their relative contribution would have been greater in drier months due to the proximity of the tributaries to the high rainfall zone near the coast and the extended period of little or no flow in the Avon River.

By contrast, flows in the Avon River are estimated to have increased by 3-4 times over the past 100 years as a result of clearing of remnant vegetation (Viney and Sivapalan, in press). The clearing was particularly widespread between 1940 and 1970. The subsequent increases in runoff prompted adoption of a 'river training scheme', in which large sections of the Avon River were cleared of vegetation ('ripping' of the river bank), then straightened and deepened by bulldozer. It is now generally accepted that this procedure has had a severe impact upon the ecology of these sections of the Avon River and led to major problems with sediment erosion and riverbank stability along many parts of the river (Harris, 1996). Perhaps of even more concern is the rapid increase in salinisation, waterlogging and land degradation in the Avon River catchment, which has resulted from land clearing and reduced water loss(/evapotranspiration) as a result of removal of the remnant vegetation.

More recently, rapid growth of the city of Perth has led to the transformation of traditionally rural or natural catchments to urban catchments (e.g. Ellen Brook), as well as increasing population densities in land adjacent to the Swan River. Catchment models (Sivapalan, pers. com.) indicate corresponding increases in stormflow and more rapid response of tributary inflows to rainfall due to the increased fraction of impermeable surfaces in urban areas. Further, development of marinas and boat harbours in the upper estuary, while not unduly influencing the residence time over the entire estuary, may potentially lead to localised variations in water residence time, at least within the semi-enclosed regions.

METHODS Daily streamflow data were obtained from The Water and Rivers Commission Regional Services gauges for the Avon River, Ellen Brook, Helena River, Jane Brook, and Susannah Brook. The sum of these inflows contributes most of the flow to the upper Swan River (Peters and Donohue, in press). The six monitoring sites used in the analysis of this study were distributed roughly equidistantly from ~25 km upstream of the estuary mouth to ~ 40km upstream, just above the convergence with Helena River (see Fig. 1). Cell counts of the phytoplankton community were made by the Water and Rivers Commission Phytoplankton Ecology Unit. Counts were performed on depth-integrated triplicate water samples, which were taken with a polyethylene hose-pipe sampler to 6m depth or to within 0.5m of the bed. Samples were preserved with Lugol's iodine solution at a ratio of 1:100. Subsamples of 1 mL were transferred to Sedgwick Rafter Cells for examination at 125- 200x magnification. Counts of 300 cells or ten grids were made, and identification was performed to genus or family level. Salinity profiles were recorded at each station with a Hydrolab Datasonde multiprobe.

To appear in Proceedings, 3rd International Hydrology and Water Resources Symposium (Hydro 2000), Vol 1, pp. 114- 119, 2000. preprint – 4 of 7

RESULTS Streamflow was summed for the Avon River, Ellen Brook, Helena River, Jane Brook, and Susannah Brook, the major tributaries to the upper Swan River estuary. Figure 2 shows a representative subset of the data to illustrate that the great majority of the flow occurred in winter and spring, but that there were wide inter- annual fluctuations (Fig. 2). Variations in salinity in the upper estuary were correspondingly large, ranging from 0.5 to 36 psu. These gradients had an important influence on the phytoplankton community composition. Figure 3 illustrates the three main phytoplankton groups recorded in the upper estuary in relation to surface salinity. Few other phytoplankton groups were recorded in high numbers in the estuary although crytophyte cells occasionally exceeded 20% of the total count. In figure 3 an upper envelope is placed on cell counts of diatoms, chlorophytes and dinoflagellates to illustrate how each phytoplankton group falls into a distinct salinity range. Diatoms appear to be able to attain moderate numbers over almost the entire range of recorded salinities (and flows), but a distinct transition between freshwater diatoms and marine diatoms (predominantly Skeletonema costatum) is evident in the trough of cell counts at a salinity of ~12 psu (Fig. 3). Dinoflagellates attained blooms levels (arbitrarily assigned at 40,000 cells ml-1) over a wide range of salinities also, but were present in low numbers at salinities below 7 psu or above 33 psu. Dinoflagellate blooms were restricted to flows of less than 15 ML d-1. Chlorophytes clearly had lower tolerance to salinity than the other two groups and formed blooms only at salinities between 3 and 12 psu. Chlorophyte blooms occurred at flows of between 40 and 1000 ML d-1.

The tolerance of these phytoplankton groups to different flow rates and salinities appears to dominate the observed sequence of succession, although nutrients (e.g. nitrogen; Thompson and Hosja, 1996) certainly play a role in the cell numbers attained. Chlorophyte blooms occur in the upper estuary in spring, just prior to intrusion of the salt wedge, when there is moderate flow and low salinity. Chlorophytes are generally succeeded by marine diatoms, while dinoflagellates can be present at bloom levels later in summer and through autumn, as flows recede. The annual sequence of succession is completed when winter rains commence and freshwater diatoms become dominant.

300 1995 250 1996 )

-1 1997 s 3 200

150

Streamflow (m Streamflow 100

50

0 0 30 60 90 120 150 180 210 240 270 300 330 360 Day of year

Figure 2. Streamflow in the Avon River over three consecutive years.

To appear in Proceedings, 3rd International Hydrology and Water Resources Symposium (Hydro 2000), Vol 1, pp. 114- 119, 2000. preprint – 5 of 7

DISCUSSION

The hydrology of the Swan River estuary is very different today to that of 100 years ago. As a result of dredging at Fremantle phytoplankton communities are now dominated by marine diatoms and estuarine dinoflagellates in both the upper and lower basins for most of the year. Previous studies (e.g. Hodgkin and Hesp, 1998) indicate that saline intrusion would originally have been confined largely to deeper waters of the lower basin. This net result of this change may arguably be beneficial, despite the initial displacement of freshwater species, as increased flushing with low nutrient seawater imposes a direct constraint on bloom development (Chan and Hamilton, 2000). This is of great significance at a time when nutrient levels in freshwater tributaries have increased markedly (Donohue et al., in press).

Indirect evidence of beneficial effects of seawater flushing may be gained from three examples. On 25 February 2000 flow in the Avon River peaked at 310 m3s-1 in response to widespread rainfall throughout the Avon catchment three days earlier (Hamilton, 2000). This inflow exceeded peak flows of recent years (cf. Fig. 2) and displaced all the marine water from the upper basin and most from the lower basin for a period of almost 1-month. This produced conditions very unusual for summer in the Swan River in its present form, and resulted in a major bloom of the blue-green alga Microcystis aeruginosa in response to the high nutrient levels associated with the freshwater runoff, and optimal light and temperature conditions of late summer. The bloom subsided with the re-intrusion of salt water to the system due to seawater flushing.

The second example relates to the Canning River, where enclosure of freshwaters by a weir has resulted in severe, recurrent blue-green algal blooms (Anabaena spp.) in the region above the weir from spring to autumn (Waite, 1998). The third example is in the -Harvey Estuary, 80 km south of the Swan River, in which severe spring to summer blue-green algal blooms (Nodularia spp.) occurred for more than a decade from 1978. In 1994 an artificial channel was connected between the Harvey Estuary and the ocean to enhance flushing of the estuary by marine water, and this eliminated the blooms (Lord et al., 1998). In summary, it would be expected that blooms of freshwater chlorophytes and cyanobacteria are more likely to occur in systems which are not well flushed with seawater and are subject to increased nutrient inputs from changes to land use.

The beneficial effects of increased seawater flushing of the Swan River and Peel-Harvey Estuaries may be to some extent be counteracted by reduced capacity of these systems to act as filters for the adjoining coastal waters (cf. Fisher et al., 1988). Both estuaries represent important components of the nutrient budget of the oligotrophic waters of the local coastal zone, and some impacts on productivity of this zone are expected, depending on rates of flushing of the coastal waters.

The impacts of changes in freshwater runoff to the Swan River are difficult to judge. The net result of vegetation clearing in the Avon River and damming of tributaries from coastal catchments is likely to be greater seasonality, consisting of a greater duration of low freshwater inputs to the estuary, but greater volumes entering the estuary in the wet seasons of winter and spring.

Changes to the hydrology of the Swan River catchment areas thus have direct and indirect implications for phytoplankton succession and phytoplankton blooms, not only through the effects on nutrient loads, but also the effects of salinity and flow rates in the River.

ACKNOWLEDGMENTS

The authors thank the Water and Rivers Commission for the data made available for this analysis.

To appear in Proceedings, 3rd International Hydrology and Water Resources Symposium (Hydro 2000), Vol 1, pp. 114- 119, 2000. preprint – 6 of 7

REFERENCES

Ackroyd, D. R., Millward, G. E. and Morris, A. W. 1987. Periodicity in the trace metal content of estuarine sediments. Oceanologica Acta 10, 161-168.

Boynton, W. R., Hollibaugh, J. T., Jay, D., Kemp, M., Kremer, J., Simenstad, C., Smith, S. V. and Valiela, I. 1992. Understanding changes in coastal environments: The LMER program. Eos Trans., AGU, 73(45), 481, 484-485.

Cloern, J. E. 1996. Phytoplankton bloom dynamics in coastal ecosystems: a review with some general lessons from sustained investigation of San Francisco Bay, California. Rev. Geophys., AGU, 34, 127-168.

Donohue, R. Davidson, W. A., Peters, N. E. Nelson, S. and Jakowyna, B. Trends in total phosphorus and total nitrogen concentrations of tributaries to the Swan-Canning Estuary, 1987 to 1998. Hydrol. Proc. (in press).

Fisher, T. R., Harding, L. H., Stanley, D. W. and Ward, L. G. 1988. Phytoplankton, nutrients and turbidity in the Chesapeake, Delaware and Hudson estuaries Est. Coast. Shelf Sci., 27, 61-93.

Geyer, W. R. and Farmer, D. M. 1989. Tide induced variation of the dynamics of a salt wedge estuary. J. Phys. Oceanogr., 19, 1060-1072.

Hamilton, D. P., Thompson, P. A., Kurup. R. and Horner-Rosser, J. 1999. Dynamics of dinoflagellate blooms in the Swan River Estuary, in: McComb, A. J. and Davis, J. A. (Eds), Proceedings of the Vth International Wetlands Conference, Gleneagles Press, Adelaide, South Australia. pp. 273-286.

Hamilton, D. P. 2000. Record summer rainfall induced first recorded major cyanobacterial bloom in the Swan River. J. Env. Eng. Soc., Inst. Eng., 1(1), 25.

Hamilton, D. P., Chan, T., Robb, M. S., Pattiaratchi, C. B. and Herzfeld, M. The hydrology of the upper Swan River estuary with focus on an artificial destratification trial. Hydrol. Proc. (in press).

Hodgkin, E. P. and Hesp, P. 1998. Estuaries to salt lakes: Holocene transformation of the estuarine ecosystems of south-western Australia. Mar. Freshwat. Res., 49(3), 183-201.

John, J. 1994. Eutrophication of the Swan River Estuary, Western Australia and the management strategy, in: Mitsch, W. J. (Ed.), Global Wetlands: Old World and New, Elsevier. pp. 749-757.

Linderfelt, W. R. and Turner, J. V. Interaction between shallow groundwater, saline surface water and nutrient discharge in a seasonal estuary: The Swan-Canning system. Hydrol. Proc. (in press).

Lord, D.A. & Associates Pty Ltd. 1998. Dawesville Channel Monitoring Programme Technical Review. Water and Rivers Commission Report WRT 28. Perth, Western Australia. 200 pp.

Malone, T. C., Crocker, L. H., Pike, S. E. and B. W. Wendler, 1988. Influences of river flow on the dynamics of phytoplankton production in a partially stratified estuary. Mar. Ecol. Prog. Ser., 48, 235-249.

Mortimer RJG. Krom MD. Watson PG. Frickers PE. Davey JT. Clifton RJ. Sediment-water exchange of nutrients in the intertidal zone of the Humber estuary, UK. Marine Pollution Bulletin. 37(3-7):261-279, 1998.

Harris, T. F. W., 1996. The Avon: An Introduction. Water and Rivers Commission Report, 122pp.

Smetacek, V., von Bodungen, B, von Brockel, K and Zeitschel, B. 1976. The plankton tower II. Release of nutrients from sediments due to changes in the density of bottom water. Marine Biology, 34, 373-378.

To appear in Proceedings, 3rd International Hydrology and Water Resources Symposium (Hydro 2000), Vol 1, pp. 114- 119, 2000. preprint – 7 of 7

Stephens, R. and Imberger, J. 1996. Dynamics of the Swan River estuary: the seasonal variability, J. Mar. Freshwat. Res., 47, 517-529.

Thompson, P. A. and Hosja, V. 1996. Nutrient limitation of phytoplankton in the upper Swan River Estuary, Western Australia, J. Mar. Freshwat. Res., 47, 659-667.

Thompson PA. Spatial and temporal patterns of factors influencing phytoplankton in a salt wedge estuary, the Swan River, Western Australia. Estuaries. 21(4B):801-817, 1998 Dec.

Viney, N. R. and, Sivapalan, M. Modelling catchment processes in the Swan-Avon River basin, Hydrol. Proc. (in press). Waite, Anya. 1998. Report on nutrient fluctuations in the Canning River during a cyanophyte bloom 1997/98. Water and Rivers Commission Report, December 1999. 29pp.

To appear in Proceedings, 3rd International Hydrology and Water Resources Symposium (Hydro 2000), Vol 1, pp. 114- 119, 2000.