Identifying drought refuges in the Wakool system and assessing status ...

Identifying drought refuges in the Wakool system and assessing status of fish populations and water quality before, during and after the provision of environmental, stock and domestic flows Dean Gilligan, Adam Vey and Martin Asmus NSW Department of Primary Industries Aquatic Ecosystems Research Batemans Bay Fisheries Office PO Box 17, Batemans Bay, NSW, 2536 Australia

Murray-Darling Basin Authority Project No. MD1046

June 2009 NSW Department of Primary Industries – Fisheries Final Report Series No. 110 ISSN 1449-9967

Identifying drought refuges in the Wakool system and assessing status of fish populations and water quality before, during and after the provision of environmental, stock and domestic flows. June 2009 Authors:

D. Gilligan, A. Vey and M. Asmus

Published By:

NSW Department of Primary Industries (now incorporating NSW Fisheries)

Postal Address:

Cronulla Fisheries Research Centre of Excellence, PO Box 21, NSW, 2230

Internet:

www.dpi.nsw.gov.au

Cover photo:

Environmental flow breaching a sandbar and entering a pool at ‘Merran Downs’, Wakool River, 12 January 2008 (Photo: Adam Vey).

© NSW Department of Primary Industries and the Murray-Darling Basin Authority. This work is copyright. Except as permitted under the Copyright Act, no part of this reproduction may be reproduced by any process, electronic or otherwise, without the specific written permission of the copyright owners. Neither may information be stored electronically in any form whatsoever without such permission.

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ISSN 1449-9967 (Note: Prior to July 2004, this report series was published as the ‘NSW Fisheries Final Report Series’ with ISSN number 1440-3544)

Contents

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TABLE OF CONTENTS TABLE OF CONTENTS.................................................................................................................................I LIST OF TABLES.......................................................................................................................................... II LIST OF FIGURES ....................................................................................................................................... II ACKNOWLEDGEMENTS..........................................................................................................................III NON-TECHNICAL SUMMARY ................................................................................................................ IV 1.

BACKGROUND AND CONTEXT ...................................................................................................... 6

2.

METHODS.............................................................................................................................................. 9 2.1. 2.2. 2.3. 2.4. 2.5. 2.6.

3.

MAPPING AQUATIC REFUGIA WITHIN THE SYSTEM ............................................................................. 9 SAMPLING FISH ASSEMBLAGES WITHIN REFUGIA ............................................................................... 9 SAMPLING WATER QUALITY WITHIN REFUGIA.................................................................................. 12 QUANTIFYING AQUATIC HABITAT AVAILABILITY WITHIN REFUGIA .................................................. 12 WATER QUALITY SURVEILLANCE AT THE FLOW FRONT ................................................................... 13 POST-FLOW FISH ASSEMBLAGE ASSESSMENTS ................................................................................. 13

RESULTS.............................................................................................................................................. 15 3.1. DISTRIBUTION, EXTENT AND SCALE OF PRE-FLOW DROUGHT REFUGIA ............................................ 15 3.2. FISH ASSEMBLAGES, WATER QUALITY AND HABITAT WITHIN PRE-FLOW DROUGHT REFUGIA ........... 16 3.2.1. Pre-flow fish assemblages..................................................................................................... 16 3.2.2. Pre flow water quality........................................................................................................... 18 3.2.3. The effects of habitat characteristics on the quality of refugia ............................................. 19 3.3. WATER QUALITY SURVEILLANCE AND OBSERVATIONS AT THE FLOW-HEAD DURING THE ENVIRONMENTAL RELEASE PERIOD.................................................................................................. 20 3.3.1. Case study: The Wakool River – Erigen Creek confluence................................................... 22 3.4. POST-FLOW FISH COMMUNITY AND WATER QUALITY RESPONSES AT DROUGHT REFUGIA ................ 23 3.4.1. Changes in abundance and prevalence and recruitment responses of fish .......................... 23 3.4.2. Post-flow responses of water quality within refugia ............................................................. 26 3.4.3. Re-distribution of fish among refugia ................................................................................... 31

4.

DISCUSSION........................................................................................................................................ 32 4.1.

CONCLUSIONS ................................................................................................................................. 34

5.

REFERENCES ..................................................................................................................................... 36

6.

APPENDICES....................................................................................................................................... 39

Project No. MD1046: Wakool environmental flow surveillance and monitoring

Gilligan, Vey & Asmus

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Contents

LIST OF TABLES Table 1. Table 2. Table 3. Table 4. Table 5.

Table 6.

The locations of fish sampling sites within the Wakool River, Merran Creek and Niemur River. ......................................................................................................................................... 10 Size limits used to estimate the proportion of new recruits for each species. ........................... 12 Adopted acceptable water quality thresholds for fish refuges................................................... 14 Fish species collected from waterhole refugia within the Murray Riverina anabranch system in November – December 2007, priori to the arrival of environmental flows. ............. 17 Fish species known or presumed to have been historically present in the Murray Riverina anabranch system, but which were not collected during the first round of sampling of waterhole refugia....................................................................................................................... 18 Mean ± one standard deviation, minimum and maximum water quality values and depth measurements recorded at each of the 18 waterhole refugia in the Murray Riverina anabranch system prior to the arrival of environmental flows in November – December 2007........................................................................................................................................... 19

LIST OF FIGURES Figure 1. Figure 2. Figure 3. Figure 4. Figure 5. Figure 6. Figure 7. Figure 8. Figure 9. Figure 10.

Figure 11.

Figure 12. Figure 13. Figure 14. Figure 15. Figure 16. Figure 17. Figure 18. Figure 19.

Murray system monthly inflows excluding Darling inflows and Snowy diversions................... 6 The principal streams of the Murray Riverina anabranch system. .............................................. 7 Sampling locations for fish and repeat water quality monitoring locations. ............................. 10 The distribution of aquatic refugia within the Murray Riverina anabranch system on 27 November 2007. ........................................................................................................................ 15 The frequency of remnant waterholes ranging from 4,000 μS/cm) at two lower Wakool sites during pre-flow surveys (Calaroga and Tueloga) during pre-flow surveys, electrofishing was expected to be less effective and a suite of four panel nets (three 5 x 2 m panels with 38, 67 and 100 mm mesh (15 m total length)) were used in place of electrofishing. During each operation, a dip-netter removed electrofished individuals from the water and placed them in an aerated live-well (boat fishing) or bucket (backpack fishing). All individuals that could not be dip-netted but could be positively identified were recorded as ‘observed’. All electrofishing was undertaken during daylight hours. The 10 shrimp traps were set in an attempt to sample smaller fish which are sometimes under-represented in electrofishing samples. Traps were set for a minimum period of two hours whilst electrofishing was being undertaken. At the completion of each operation (electrofishing, shrimp trap or panel net), captured individuals were identified, counted, measured and observed for health conditions such as externally visible parasites, wounds or diseases using the sub-sampling procedure described in MDBC (2007) with the exception that there was no minimum length criteria used. Measurements to the nearest millimetre were taken as fork length for species with forked tails or total length for other species. Biomass was estimated from length-weight relationships presented in Table 8 of MDBC (2004). The weight of unmeasured and observed individuals was estimated using the average weight of all measured individuals of that species, for that gear type, at that site. Size limits used to categorise individuals as new recruits were based on either the size at one year or the size at sexual maturity for species that reach sexual maturity at less than one year of age (Table 2). These size limits were used as a guideline to distinguish fish which were spawned during the preceding breeding season from those that were older. All individuals greater than 200 mm in length were tagged with individually numbered dart tags so that individuals recaptured during subsequent rounds of sampling could provide information on inter-refuge movements within the system once environmental flows arrived.



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NSW Dept of Primary Industries

Table 2.

Size limits used to estimate the proportion of new recruits for each species.

Species

Estimated size at 1 year old or at sexual maturity (mm) and the source of that estimate

Native species Australian smelt Bony herring Carp-gudgeon species complex Flat-headed gudgeon Flyspecked hardyhead Golden perch Murray cod Murray-Darling rainbowfish Silver perch Alien species Common carp Eastern mosquitofish Goldfish Oriental weatherloach

40 (Pusey et al. 2004) 67 (Cadwallader 1977) 30 (Pusey et al. 2004 and NSW DPI unpublished data) 50 (Pusey et al. 2004) 40 (Pusey et al. 2004) 75 (Mallen-Cooper 1996) 235 (Rowland 1998) 45 (Pusey et al. 2004: for M. duboulayi) 75 (Mallen-Cooper 1996) 200 (Brown et al. 2003) 20 (McDowall 1996) 100 (Brumley 1996) 100 (Koster et al. 2002)

NOTE: Pusey et al. (2004) presented length data as standard length. Data from Pusey et al. (2004) in this table reflects the average of the mean male and female lengths presented, with rounding up to the nearest 5 mm increment to reflect either total length or fork length.

2.3.

Sampling water quality within refugia

Water quality parameters (temperature (oC), pH, dissolved oxygen (mg/L), conductivity (μS/cm) and turbidity (NTU) were recorded using a Horiba U10 water quality meter at each site on the date of sampling. Water quality was assessed at 0.2 m below the water surface (the average of two measurements) and at 1 m depth intervals to the stream bed (one measurement only) in order to quantify any stratification within the water column. The water column was classed as stratified if any one of temperature, pH, dissolved oxygen or conductivity declined by more than 25% of the surface value at depth. 2.4.

Quantifying aquatic habitat availability within refugia

Aquatic habitat features (riparian and instream vegetation, substratum, mesohabitat and instream cover variables) were recorded as present or absent within each of the replicate electrofishing operations, each corresponding to a transect of ~ 43 ± 1 m (mean ± SE). Aquatic habitat availability was then quantified as the proportion of operations at each site where each habitat feature was present (i.e. if native riparian trees were present in 9 of 12 replicate operations, then they would be scored as 9 / 12 = 0.75). Additionally, depth and width were recorded for each electrofishing operation and averaged across operations and the maximum depth across the entire sampled site was recorded. Flow velocity was assessed as either: no flow, slow, medium or fast for each operation and the modal velocity (the value that occurs most frequently) was calculated. Three fish assemblage parameters (native species richness, total native abundance and total native biomass) were recorded from 16 of the 18 drought refugia prior to arrival of the environmental flows. These calculations were not done for Tueloga or Calaroga because no electrofishing was done at these sites, making direct comparisons with the other sites problematical. These fish assemblage parameters were then regressed on eleven habitat availability values (availability of




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sand, mud/silt and clay substratum, availability of riparian trees, shrubs and grass, availability of emergent and submerged macrophytes, availability of filamentous algae and biofilms, availability of timber cover) and two physical dimensions of each waterhole (average depth and wetted width). This analysis was used to identify those aquatic habitat features that determine or relate to the ‘quality’ of drought refugia within the anabranch system. The remaining fourteen habitat variables recorded were either invariable across refugia or were correlated with one of these variables listed above, so were not included in the analyses. All but average depth and native abundance approached normality and were not transformed prior to analysis, while these two variables were normalised with a log10 transformation. Multiple linear regression was undertaken separately for each of the three fish assemblage parameters using Genstat 10.1. The best regression model was identified based on Mallow’s Cp (Quinn and Keough 2002) and the significance of this best-fit model is reported without any adjustment for the experiment-wide error rate. 2.5.

Water quality surveillance at the flow front

Water quality surveillance using a Horiba U-10 meter was conducted from 28 December 2007 to 26 February 2008. Data were recorded daily through December – January and weekly throughout February at 21 sites (17 on the Wakool River and 4 on the Niemur River). Additional recordings were also made in association with the progression of the flow-head in the Wakool River channel. A total of 114 water quality assessments were undertaken (Appendix 2). Water quality thresholds were developed to assist in the identification of sites where the risk of fish mortalities prevailed (Table 3). These precautionary parameters were adopted from existing knowledge of fish kills in NSW (NSW Fisheries, 2000) and published observations of the behaviour of fish during incidents of poor water quality in the field (see Table 3 for references). The daily water quality readings with respect to the thresholds and general field observations were communicated to the ‘Wakool System Flow Steering Group’ set up by the MDBC both electronically (Appendix 3) and through regular teleconferences. DPI established contact with six key landholders and received timely information from them regarding the progress of flows and relevant fish habitat management issues. 2.6.

Post-flow fish assemblage assessments

A second round of fish surveys was conducted between 4 March and 25 March 2008, soon after the cessation of delivered flows in Merran Creek, the Niemur River and the Wakool River progressively. These post-flow surveys were intended to assess the short-term response of fish populations to flow provision. The particular questions addressed were: i. Had there been a re-distribution of fish among refugia; ii. Was this related to pre-flow water quality conditions; iii. Was movement in an upstream or downstream direction; iv. Had fish exited the system when connectivity was restored; v. Had fish been drawn to enter the system from inflows or once effluent flows reentered the Murray River? A third round of fish surveys was conducted between 12 May and 2 July 2008, approximately 2 months following cessation of flows. This round of data collection was intended to assess the recruitment response to flow provision, as any fish spawned during the flow period would have had sufficient time to grow to a size at which the sampling methods were capable of collecting them effectively. Additionally, the persistence of those changes in fish assemblages and water quality variables observed during the second round of sampling could be assessed.



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At most sites, the same suite of sampling equipment used in the baseline surveys was re-deployed in the second and third sampling rounds. However, given the increased water levels and/or reduced conductivities at some sites, some re-allocation of sampling gears was necessary. At the two sites that were affected by saline water during pre-flow sampling, Calaroga and Tueloga, reduced conductivity during the post-flow sampling rounds allowed the use of electrofishing methods during the second and third sampling occasions. Consequently, both electrofishing and panel netting was used at these two sites during these rounds to retain inter-round consistency. Subsequent comparisons only used the subset of data collected using consistent gear types at these sites. As in the Sustainable Rivers Audit, no distinction was made between data collected using the three forms of electrofishing sampling (large boat, small boat and backpack electrofishing) as all three are considered to be equally effective at representing fish communities present at the scale of sites where each electrofishing method is used 1. In the second and third round of sampling, water quality and habitat parameters were recorded at each sampling event as per the pre-flow baseline surveys. Surface water quality of the 17 refugia that received flow (i.e., all except Burswood Park) were compared before flows arrived and soon after flows ceased, and before flows arrived and ~ 2 months after flows ceased using paired t-tests. Only dissolved oxygen concentration, pH and electrical conductivity were compared. Table 3.

Adopted acceptable water quality thresholds for fish refuges. (Adapted from NSW Fisheries, 2000).

Water quality parameter

Adopted ‘stress’ thresholds

Comment

Temperature

As suggested by McKinnon (1997), but will vary by species.

Dissolved oxygen

< 5oC or > 30oC < 5 mg/L

pH

< 6 and > 9

Electrical conductivity

> 5,000 μS/cm

Turbidity

NTU > 93 or TSS > 5,000 mg/L

The absence of suitable oxygen saturation results in stress to fish and can lead to mortality. Few species and especially larger individuals can tolerate long term exposure to dissolved oxygen levels below 3 mg/L. McKinnon (1995) observed stressed Australian smelt and Common carp at 5.6 mg/L. Acidic or alkaline water is an indicator of chemical toxicity, which can be fatal for fish. Koehn and O’Connor (1990) report no notable impact on native fish within this range. Micro siemens (μS) per cm is a measure of conductivity, which is increased proportionally with the increased salinity of water. McCarthy et al. (2003) observed a fish-kill of Common carp at 26,000 μS/cm. McCarthy et al. (2003) report a possible restriction on larval survival and recruitment of un-specked hardyhead and carp-gudgeons at 10,000 μS/cm. Ellis et al. (2004) reported survival of Murray cod at 4,000 μS/cm. Walker and Hillman (1982) and Shiel et al. (1982) refer to turbidity values of around 64 and 70 NTU as high and Geddes (1984) considers 93 NTU as extreme in terms of its impact on primary production.

1

Sites where electrofishing effort differed between sampling occasions were: Lynton; 1st sample – backpack electrofishing (BP), 2nd sample – small boat electrofishing (SB) – 3rd sample, BP, La Rosa; 1st - SB/BP hybrid, 2ndand 3rd large boat electrofishing (LB), Merran Creek Bridge; 1st and 2nd – SB, 3rd – BP, Site Tueloga Road Bridge; 1st – BP, 2nd – LB, 3rd – BP, Burswood Park; 1st – SB, 2nd and 3rd – BP, Ventura; 1st – SB, 2nd and 3rd – LB and Niemur Valley; 1st – SB/BP hybrid, 2nd and 3rd – SB).




3.

RESULTS

3.1.

Distribution, extent and scale of pre-flow drought refugia

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The distribution of surface water within 1,132 km of waterways in the Murray Riverina anabranch system was mapped from the air on 27 November 2007 (Figure 4). The bottom 45 km of the Wakool River, downstream of Stony Crossing (latitude: -35.02, longitude 143.55), is effectively permanently inundated by waters backed-up from its junction with the Murray River downstream. As at 27 November, stock and domestic flows released since 16 November 2007 into Merran Creek via the Old Merran Cutting Offtake and Waddy Cutting Offtake had travelled 74 km. Flows released since 20 November 2007 into Yallakool Creek via the Yallakool Creek regulator and Yallakool Escape had travelled 42 km and flows released into the Wakool River via the Wakool River Escape and Wakool Town Escape had travelled 28 km. Combined, these flows had replenished around 13% of the major stream network within the system. A further 83% of the anabranch system had not received any flow since August 2007. Of this, 484 km (43%) was dry, 239 km (21%) consisted of shallow and inconsistent surface water and 220 km (19%) consisted of waterhole refugia assumed to be sufficient to sustain populations of large fish species. There were 68 remnant waterholes in total, with an average (± SD) length of 3.03 ± 4.30 km. The largest waterhole consisted of a continuous 19.54 km reach at the Wakool River-Merran Creek junction. However, the distribution of refugia size was heavily skewed, with 38% of waterholes less than 1 km long and 62% were less than 2 km long, indicating that a majority of refugia were small (Figure 5).

Figure 4.

The distribution of aquatic refugia within the Murray Riverina anabranch system on 27 November 2007.



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30

Number of refugia

25

20

15

10

5

0