Fish and freshwater crayfish communities of the Blackwood River: migrations, ecology and the influence of surface and groundwater

Section 1 – Migration patterns of the fish and crayfish fauna of the Blackwood River South‐western Australia has a highly endemic freshwater aquatic fauna, with 80% of the fishes and 100% of the crayfishes found nowhere else. Each of the endemic fishes is found within the Blackwood River catchment, with two being restricted to the floodplains of the Scott River; a major tributary of the Blackwood. Salinisation of the catchment has compromised the natural ranges of many of the fishes, with many of the non‐halotolerant species now restricted to forested tributaries within the lower catchment and in the section of the main channel where salinity is reduced as a consequence of discharge from the Yarragadee and Leederville aquifers. Prior to this study, only snap‐shot fish surveys around the major regions of Leederville and Yarragadee groundwater discharge into the Blackwood River existed allowing only a limited understanding of the ecology of the fish communities and their relationship with key environmental variables; particularly surface and groundwater hydrology. This knowledge is important in the light of potential future increased groundwater extraction and climate change. To further the understanding of the fish communities of this region, Section 1 of this study examined the temporal migration patterns of fish and freshwater crayfish in this zone of the Blackwood catchment. Specifically, upstream and downstream migration patterns of fishes in the Blackwood River and its tributaries were examined and related to a number of key environmental variables, such as surface and groundwater discharge. Predictions of the effects on fauna by projected changes in environmental variables, for example, due to aquifer draw‐down (e.g. reduced discharge and increased salinity) were examined. In order to determine fish migrations within and outside of the major area of groundwater discharge, four main channel sites (one receiving the entire Yarragadee discharge, one at the upstream point of the discharge, and two upstream of the discharge) were monitored. Furthermore, sites within four tributaries were also monitored for patterns of fish migration and community structure in relation to environmental variables; namely surface water reliant seasonal systems, i.e. Rosa Brook, Layman Brook and McAtee Brook, and a perennial groundwater fed system, i.e. Milyeannup Brook. Migration and population demographics were examined on eight occasions between October 2005 and September 2006. A variety of sampling methods were utilised including fyke netting, seine netting, trapping and electrofishing. Substantial differences in fish densities and migration patterns existed between and within the main channel and major tributaries. The main channel was dominated by estuarine and salt‐tolerant species at all sites. However, main channel sites receiving most groundwater discharge (i.e. receiving both Leederville and Yarragadee Aquifer discharge) had much greater abundances of non‐salt tolerant freshwater native species than those sites upstream of the Yarragadee discharge. This suggests that although the fish community in the main channel may have changed to primarily salt tolerant species in response to increasing salt levels, fresh groundwater input in summer (when many tributaries cease to flow or dry completely), may be enabling those species to continue to survive in the main channel. The study also recorded a considerable upstream migration of the Freshwater Cobbler at all main channel sites in spring and summer; a period that coincided with their spawning. It was found that upstream Freshwater Cobbler migrations in main channel sites were highly correlated to summer discharge. This species is considered to be ideal for long‐term monitoring of river connectivity. The Marron population was assessed in the main channel and a slightly higher relative abundance (although not statistically significant) was recorded within sites receiving most groundwater discharge (i.e. both Leederville and Yarragadee Aquifer discharge) than those upstream. Marron catches have recently been found to be positively correlated with river flow and this has implications for the recreational fishery within the Blackwood River under reduced flow scenarios. Considerable differences in the timing and strengths of fish migrations were recorded between tributaries for the Western Minnow, Nightfish and Western Pygmy Perch, that utilised all four tributaries to varying degrees. It was found that the tributaries act as the major spawning habitats for these species and the section of the main channel that receives the most groundwater discharge acts as a refuge to the summer contraction or drying of most of these systems. Significant differences in strength of migrations between tributaries for some native freshwater species were explained by environmental variables during the peak flow period. For example, downstream and upstream migration strengths of the Western Minnow in the four tributaries were highly correlated with stream discharge whereas upstream migrations of Western Pygmy Perch and Nightfish were correlated with dissolved oxygen levels and earlier breeding and recruitment of Western Minnows occurs in the perennial Milyeannup Brook. Milyeannup Brook is one of only two (along with Poison gully) perennially flowing tributaries in this region of the Blackwood and are directly reliant on Yarragadee Aquifer discharge. It was apparent that this system is of critical conservation importance as it houses the only population of the Balston’s Pygmy Perch in the Blackwood River catchment (listed as Vulnerable under the EPBC Act 1999). This study found a clear upstream and downstream spawning migration of Balston’s Pygmy Perch in this system and found only limited upstream movement from the main channel suggesting it is a crucial refuge to Balston’s Pygmy Perch in the Blackwood River catchment. By mapping fish distributions along its length in summer, the study also found that Balston’s Pygmy Perch only utilised the lower ~1300m of the ~2500m base flow stream length suggesting that only ~52% contained suitable habitat (e.g. adequate depth) for occupation. The minimum population of this species in this system was found to be ~380 ±42 fish based on their density. This low population minimum makes this species particularly vulnerable to potential habitat decline; particularly if main channel summer water quality decline exceeds this species environmental tolerance. A number of key knowledge gaps pertaining to the ecology of the fish communities are identified. Major knowledge gaps include determining the degree of interannual variation in groundwater reliance of these communities, salinity tolerances of these species, and identifying critical riffle zones in the Blackwood River that are important in maintaining river connectivity. Section 2 – Crayfish burrowing activity in the region of the Yarragadee Discharge Zone, Blackwood River A study of the burrowing activity of freshwater crayfish in the region of the Yarragadee Discharge Zone was conducted over the period of one year, starting September 2005. The aims of the study were to determine seasonal effects on burrowing activity for freshwater crayfish species in response to groundwater and surface water changes, and to relate these to emergent crayfish. In addition, a pilot study of the chemical characteristics of surface and groundwater in the area was undertaken to determine if discharge from the Yarragadee was detectable and if it was a migratory cue for freshwater crayfish. Transects were set up in creeks receiving input from the Yarragadee (Layman Brook, Poison Gully and Milyeannup Brook), as well as in control sites upstream (McAtee Brook) and downstream (Rosa Brook). Burrowing density and activity were monitored from October 2005 to September 2006, as well as basic surface water and groundwater physicochemistry. In addition, observations were made of emergent crayfish during the day and at night. The study area appears to be typical burrowing habitat for south‐western Australian freshwater crayfish. Four species of freshwater crayfish were been identified: Marron (Cherax cainii), Gilgie (C. quinquecarinatus), Restricted Gilgie (C. crassimanus) and Koonac (C. preissii). Burrows and burrowing activity were highly seasonal and provide baseline data on freshwater crayfish responses to declines in surface and groundwater. The very dry autumn and early winter experienced in 2006 resulted in a slower than usual recovery of water levels (i.e. water levels experienced in September 2005 were much higher than those found in the corresponding month in 2006). While some methodological problems were encountered (i.e. species specific burrowing behaviour could not be discerned), some generalisations are possible, including: - burrowing activity increases in response to receding water levels/tables; - the depth to which crayfish burrow can be gauged, at least in, part by the nature of the soil extruded from the burrow; - ephemeral tributaries may be important for breeding (i.e. for Gilgies); and Gilgies may have an upstream (out of main channel) migration for breeding and releasing juveniles; - smaller Marron individuals use permanent flows out of the main Blackwood River channel; - Koonacs are more likely to occur in habitats with a deeper reach to the water table; - the Restricted Gilgie may have resident populations in the two permanent streams receiving Yarragadee discharge throughout the year. Future monitoring of transects or other sites can test the following hypotheses: A. If groundwater decline in Milyeannup Brook and Poison Gully is extending beyond historical ranges then the burrowing activity of freshwater crayfish will produce soil from a lower stratigraphic soil layer than previously observed. B. If groundwater decline is extending beyond historical ranges, then periods of burrowing activity will occur earlier in spring, and burrows will open later in the autumn or winter. Water samples were also collected in November/December 2005 before surface waters had receded, where the influence of groundwater discharge was relatively minimal, and in March 2006 when groundwater discharge was a more significant contributor to surface waters. The elemental suites of samples from transect surface waters, and other selected sites were determined. The pilot study of elemental water chemistry demonstrated the potential for characterising the Yarragadee discharge. In addition, high S:(Ca+Mg) ratios in Poison Gully and Milyeannup Brook indicate poor buffering and, if confirmed, may show potential for acidification should sediments become exposed due to drought and/or groundwater decline