Effect of Tide on Water Quality of Jones Creek, Darwin Harbour

Department of Land Resource Management

Effect of tide on water quality of Jones Creek, Darwin Harbour.

Report No. 02/2015D

Julia Fortune and Nathalie Mauraud

Aquatic Health Unit Department of Land Resource Management

http://www.lrm.nt.gov.au Aquatic Health Unit. Department of Land Resource Management. Palmerston NT 0831. Website: www.nt.gov.au/lrm/water/aquatic/index.html

Disclaimer: The information contained in this report comprises general statements based on scientific research and monitoring. The reader is advised that some information may be unavailable, incomplete or unable to be applied in areas outside the Darwin Harbour region. Information may be superseded by future scientific studies, new technology and/or industry practices.

Copyright protects this publication. It may be reproduced for study, research or training purposes subject to the inclusion of an acknowledgement of the source and no commercial use or sale.

This report should be cited as:

Fortune, J and Mauraud, N.(2015). Effect of tide on water quality of Jones Creek, Darwin Harbour. Report No. 02/2015D. Department of Land Resource Management, Aquatic Health Unit. Palmerston, NT.

Acknowledgements:

Thanks to Matthew Majid and Andrew Gould of the Aquatic Health Unit for their technical support during field campaigns. Simon Townsend (DLRM) provided helpful comments that improved the report. Contents

1. SUMMARY ...... i-ii 2. INTRODUCTION ...... 1 2.1 Objectives ...... 1

3. METHOD ...... 3 3.1 Field stations and sampling ...... 3

3.2 Field collection ...... 4

3.3 Sample analysis ...... 5

4. RESULTS AND DISCUSSION ...... 6 4.1 Discrete sampling ...... 7

4.1.1 Physico-chemical results...... 7

4.1.2 Nutrient results ...... 9

4.2 Variability of water quality indicators over tidal cycles ...... 10

4.2.1 Temperature ...... 19

4.2.2 pH ...... 19

4.2.3 Electrical conductivity ...... 20

4.2.4 Dissolved oxygen ...... 20

4.2.5 Turbidity ...... 22

4.2.6 Chlorophyll Fluorescence ...... 23

4.3 Hysteresis analysis for indicative neap and spring events...... 24

4.3.1 Temperature ...... 25

4.3.2 pH ...... 26

4.3.3 Conductivity ...... 26

4.3.4 Dissolved oxygen ...... 26

4.3.5 Turbidity ...... 26

4.3.6 Chlorophyll-a ...... 26

4.3.7 Neap hysteresis plots ...... 27

4.3.8 Spring hysteresis plots ...... 28

4.4 Longitudinal variation of water quality along Jones Creek ...... 30 5. CONCLUSION ...... 32 6. REFERENCES ...... 33 APPENDIX...... 34 List of Figures

Figure 1. Darwin Harbour region and major estuarine arms entering Darwin Harbour port. Jones Creek study area within insert...... 2 Figure 2. Logger deployment sites along Jones Creek...... 4 Figure 3(a). Neap tidal stage for sampling period July 15- 20...... 6 Figure 3(b). Spring tidal stage for sampling period August 9-13...... 6 Figure 4. Typical physico-chemical conditions for neap and spring tide conditions measured in Jones Creek...... 8 Figure 5. Typical nutrient concentrations measured for neap and spring tide conditions in Jones Creek...... 9 Figure 6. Temperature, pH and conductivity measured at site 1 during neap tide ...... 11 Figure 7. Dissolved oxygen, turbidity and chlorophyll fluorescence measured at site 1 during neap tide...... 12 Figure 8. Temperature, pH and conductivity measured at site 2 during neap tide...... 13 Figure 9. Dissolved oxygen, turbidity and chlorophyll fluorescence measured at site 2 during neap tide...... 14 Figure 10. Temperature, pH and conductivity measured at site 3 during neap tide...... 15 Figure 11. Dissolved oxygen, turbidity and chlorophyll fluorescence measured at site 3 during neap tide...... 16 Figure 12. Temperature, pH and conductivity measured at site 2 during spring tide...... 17 Figure 13. Dissolved oxygen, turbidity and chlorophyll fluorescence measured site 2 during spring tide...... 18 Figure 14. pH vs depth during neap cycle (July 2013)...... 20 Figure 15. pH vs depth spring cycle (Aug 2013)...... 20 Figure 16. Typical modulation of dissolved oxygen with change in tide and time of day Neap tide – July...... 21 Figure 17. Typical modulation of dissolved oxygen with change in tide and time of day Spring tide– August...... 21 Figure 18. Change in turbidity with outgoing tide (Jones Creek July 15, 2013)...... 23 Figure 19. Neap tide episode examined for hysteresis analysis (shaded). July 18, 2013...... 25 Figure 20. Spring tide episode examined for hysteresis analysis (shaded). August 9, 2013...... 25 Figure 21. Neap tide hysteresis plots for site 2. a) pH, b) Temperature, c) Conductivity, d) Dissolved oxygen, e) Turbidity and f) Chlorophyll...... 27 Figure 22. Spring tide hysteresis plots for site 2. a) pH, b) Temperature, c) Conductivity, d) Dissolved oxygen, e) Turbidity and f) Chlorophyll...... 28 Figure 23. Median values for transect sites 1 to 3, Jones Creek Neap deployment July 2013. ... 31 a) Temperature, b) pH, c) Conductivity, d) Dissolved oxygen, e) Chlorophyll and f) Turbidity...... 31 1. SUMMARY

The Aquatic Health Unit of the Department of Land Resource Management (DLRM) continues to monitor the water quality of Darwin Harbour to assess the health of the estuary and its coastal waterways and report through the Darwin Harbour Report Cards and other publications. Darwin Harbour is a dynamic estuarine system influenced by freshwater inflows from major rivers such as the Elizabeth and Blackmore systems and oceanic processes such as tides. These factors, among others, lead to variability in routinely measured water quality parameters.

Tidal stage has been identified as an important factor to consider when collecting samples for water quality, however little is known about the role of tides and their influence on water quality, particularly tropical macrotidal systems.

Given the dynamic nature of the estuary, changes in water quality with factors of variation such as tide, time and location are significant. To better understand this source of variation a field survey in Jones Creek, a small tidal creek of Darwin Harbour was undertaken. During the survey, water quality in time series was recorded over neap and spring conditions to help elucidate this effect. Water quality parameters examined were temperature, pH, electrical conductivity (EC), turbidity, dissolved oxygen (DO), chlorophyll-fluorescence and photosynthetic available radiation (PAR). The key outcomes of the study are tabulated below (Table 1).

In summary, tides can have a strong influence on some water quality parameters such as EC, turbidity, pH and DO. Increased current velocity and sediment resuspension during ebb and flood tides contributes to observed patterns. While tides appear to influence some parameters, others such as temperature and DO were influenced to a greater degree by solar radiation and appear to vary as a function of the time of day in addition to tides. Longitudinal gradients were also notable with dissolved oxygen, pH, chlorophyll-a, turbidity and conductivity indicating clear spatial variation in the tidal creek.

i Table 1. Synopsis of observed effects of neap and spring tidal cycles on water quality indicators measured in Jones Creek.

Indicator Neap Spring

Clear tidal pattern Strong tidal influence Electrical conductivity

Increases to reach peak at the slack Increases to reach peak during slack of the tide. Generally higher tide. Greater variation between flood Temperature temperatures. and ebb tides. Strong tidal influence Clear temporal pattern with tide High values at high tide Turbidity Low values at low tide

Clear tidal influence Clear tidal influence pH Low values at low tide Low values at low tide High values at high tide High values at high tide

Tidal influence Tidal influence lowest value at low tide lowest value at low tide Dissolved oxygen Highest value at high tide Highest value at high tide Decrease at slack tide Decrease at slack tide

Temporal pattern Temporal pattern Decrease at slack tide Chlorophyll-a Decrease at slack tide Highest values at low tide

ii 2. INTRODUCTION

Darwin Harbour is a large macro tidal estuary of the wet-dry tropics of the Northern Territory. The estuary is a dynamic system flanked by extensive mangrove forests covering 20,400 hectares of the region and represents around 5% of the NT’s entire mangrove area (Brocklehurst and Edmeades 1996). The catchment covers an area of 3200 km2 (water and terrestrial surfaces) where the river systems of the Elizabeth and Blackmore River estuary drain into the main port of Darwin Harbour (Fig. 1). The region is also subject to increasing development with the population centres of Darwin and Palmerston comprising approximately 120,000 people and an expanding industry base.

Water quality monitoring has continued in the estuary since 1987 with water quality report cards produced annually since 2009. Tidally induced fluctuations observed in water quality and the seasonal extremes of wet and dry seasons often determine the state of water quality in Darwin Harbour. An emphasis on better understanding these factors as determinants of variation continues to underlie current monitoring effort in the region.

Tides have been identified as an important factor to consider when collecting water samples and recent standardised sampling for tide undertaken by the Aquatic Health Unit suggests that water quality is relatively stable during neap tides (Padovan, 2005; DLRM 2013; Mauraud, 2013; Fortune, 2015). Tides can significantly influence the circulation of sediments within an estuary and the degree of mixing. These advective forces can therefore drive variation in a range of water quality parameters such as salinity, turbidity, chlorophyll-a, dissolved oxygen and pH.

Jones Creek is a small tidal creek located near Channel Island in the Middle Arm of Darwin Harbour (Fig. 1 and Fig. 2). The navigable length of the creek is approximately 3.75km with a terrestrial and tidal catchment area that covers 9.25 km2 consisting of large tracts of fringing mangrove that are inundated at high tide. The level of human disturbance within the catchment is minimal. This tropical tidal creek was chosen because of the limited disturbance and accessibility to enable evaluation of water quality with tidal modulation over neap and spring conditions.

2.1 Objectives The main objective of this report is to: (a) Identify the potential impact of tide on water quality indicators measured in a tidal creek of Darwin Harbour during neap and spring tidal events using water quality loggers and (b) examine any longitudinal gradients during neap tide.

1 Figure 1. Darwin Harbour region and major estuarine arms entering Darwin Harbour port. Jones Creek study area within insert.

2 Darwin Harbour

3. METHOD

Seabird loggers were deployed at 3 sites along Jones Creek (Fig. 2; Table 1). The distance between deployment sites was roughly 780m extending from the mouth of the creek at site 1 to the upper reaches at site 3. Each sonde was attached to a cage with heavy weights, two anchors and tied to a buoy. At the end of the deployment, the sondes were collected and data downloaded from the units. Logger units were elevated 80cm from the seabed by a support frame.

3.1 Field stations and sampling

Survey time-series measurements were conducted during the dry season to minimise the confounding effects of seasonality and collect water quality data over varying tidal regimes.

Three Seabird sondes (SBE16) were deployed in Jones Creek between July 15th and July 19th during a neap tide event and one Seabird sonde was deployed between August 9th and August 13th over a spring tide. All sondes logged the following parameters for the duration of their deployment: water temperature, depth, dissolved oxygen, chlorophyll fluorescence, turbidity, PAR (photosynthetically available radiation), pH and electrical conductivity.

The July deployment occurred over a neap tide (tide range 3m at Darwin Harbour gauge at Stokes Hill Wharf) with the August deployment (tide range 7 m) undertaken during spring tide cycle conditions.

The Seabird sondes recorded data every 15 minutes for the deployment period in July and every 10 minutes for the deployment in August. Times for deployment, retrieval and location are presented in Table 2.

Table 2. Times and location of the recordings

Seabird Site Latitude Longitude Date Start Date Finish sonde site 1 SB1 -12.5499 130.87901 15/07/2013 12:15 19/07/2013 9:45 site 2 SB2 -12.554 130.88544 15/07/2013 13:00 19/07/2013 10:15 site 3 SB3 -12.5582 130.89099 15/07/2013 14:00 19/07/2013 10:45 site 2 SB2 -12.554 130.88544 9/08/2013 9:30 13/08/2013 8:50

At each site, during deployment and recovery of the Seabird loggers, surface water (approximately 0.25 m depth) was measured for pH, dissolved oxygen (% saturation),

3 conductivity and temperature using a Quanta multi-parameter probe. Turbidity was measured with a Hach turbidity meter.

Conducting these measurements allowed the assessment of the accuracy of the SBE16 data. Adjustment was made for dissolved oxygen which where erroneously low due to insufficient flushing time (fractions of second) within the logger. On average a 1.9 mg/L difference (range - 1.4 – 4.4 mg/L) was found between logger and discrete measurements for all instruments and on both sample periods. Table A1 (Appendix) outlines the difference between logger and discrete measurements taken with a Quanta instrument. Corrected values (concentration and % saturation) are presented in this report (see Table A1 Appendix). The dissolved data should only be considered in terms of showing trends rather than the actual values presented.

Figure 2. Logger deployment sites along Jones Creek.

3.2 Field collection Discrete water quality data were collected from surface waters (0.25m depth) and then analysed in the laboratory for nutrients and chlorophyll-a.

3.3 Sample analysis

Surface samples were collected in plastic bottles and stored on ice in the field prior to laboratory - - analysis. Samples were analysed for total nitrogen (TN), nitrite (NO2 -N), nitrate (NO3 -N), ammonia-N, total phosphorus (TP), and filterable reactive phosphorus (FRP). Nutrient samples for nitrite, nitrate and FRP were filtered through 0.45m filters in the field. All samples were collected, transported and stored using recommended sampling and preservation protocols and chain of custody documentation.

The chemical and nutrient analyses were carried out by Charles Darwin University (Chlorophyll- a)and Northern Territory Environmental Laboratories (All nutrients). All nutrient samples were determined using APHA standard methods.

Table 3. Laboratory methods for water quality.

Measurement Method APHA (1998) number

Nitrate Automated cadmium reduction 4500-NO3 I

Nitrite Automated cadmium reduction 4500-NO3 I

Ammonia Automated phenate method 4500-NH3 G

Total nitrogen Persulphate method 4500-N C

Total Filterable N Persulphate method (filtered sample) 4500-N C

Filterable reactive P Flow injection analysis for orthophosphate 4500-P F

Persulphate digestion followed by automated Total phosphorus 4500-P H ascorbic acid method.

Persulphate digestion followed by automated Total Filterable P 4500-P H ascorbic acid method (filtered sample).

Chlorophyll a Fluorometry (3) or spectrophotometry (H2) 10200 H (APHA 2005)

APHA (1998) unless otherwise stated. APHA (2005) for chlorophyll-a; method depends on concentration.

3.3 Statistical analysis

Data for each parameter were plotted with depth as a function of time. A number of discrete samples were collected during deployment and retrieval for neap and spring tides. Data collected for deployment sites are presented as mean concentration with standard error with the exception of pH where medians are provided. Graphs presenting each parameter measured versus depth were undertaken using SigmaPlot V12.5. Pearson product moment correlations (Pearson’s r) were performed to measure correlation between tide height and water quality variables with a

5 significance level of 0.05 applied. Characteristics of hysteresis plots were used to evaluate any temporal variation relative to the contribution of depth in association with discrete neap and spring events over the logger deployment period.

3.4 Tidal stage for sampling periods

Tidal stage data was collected from a tidal gauge located at the East Arm Port facility on Darwin Harbour. The stage height for deployment periods indicate the change in neap and spring tidal stage range (Fig. 3a and 3b).

Figure 3(a). Neap tidal stage for sampling period July 15 - 20, 2013.

Figure 3(b). Spring tidal stage for sampling period August 9-13, 2013.

4. RESULTS AND DISCUSSION

4.1 Discrete sampling

Sampling was undertaken during the deployment and retrieval of loggers at each site (1-3) during neap conditions and at site 2 during the spring tide event. Physical parameters of temperature, pH, conductivity, salinity, dissolved oxygen and turbidity were performed in addition to sampling for chlorophyll-a (Fig. 4) and nutrients (Fig. 5).

Results provide some context for typical water quality conditions associated with neap and spring conditions at the Jones Creek sites.

4.1.1 Physico-chemical results.

55000 25

20 50000

S/cm)

15 45000

Temperature ( Temperature 10

Conductivity (

40000 5

0 35000 Site 1-Neap Site 2-Neap Site 3-Neap Site 2-Spring Site 1-Neap Site 2-Neap Site 3-Neap Site 2-Spring Sites and tide Sites and tide

105 40

100 30

Salinity (ppt)Salinity

10 DissolvedOxygen (%sat) 85

0 80 Site 1-Neap Site 2-Neap Site 3-Neap Site 2-Spring Site 1-Neap Site 2-Neap Site 3-Neap Site 2-Spring

Sites and tide Sites and tide

5 1.4

1.2 4

1.0

3 g/L) 0.8

0.6 2

Turbidity (NTU) Turbidity

Chlorophyll-a ( Chlorophyll-a 0.4

1 0.2

0 0.0 Site 1-Neap Site 2-Neap Site 3-Neap Site 2-Spring Site 1-Neap Site 2-Neap Site 3-Neap Site 2-Spring

Sites and tide Sites and tide

8.5

8.0

7.5

7.0

6.5

6.0 Site 1-Neap Site 2-Neap Site 3-Neap Site 2-Spring

Sites and tide

Figure 4. Typical physico-chemical conditions for neap and spring tide conditions measured in Jones Creek.

Water temperatures for both tidal conditions were similar for the July and August period. Whilst higher pH was observed with spring tides in contrast to neap conditions at all 3 sites examined. This is likely to be related to the higher marine inflows bringing slightly more alkaline waters into the tidal creek.

Conductivity and salinity was higher with spring tide conditions in comparison to neap tidal incursion and similarly with patterns in pH can be explained by stronger inundation of marine waters. Dissolved oxygen was observed to be slightly lower with spring tide deployment and retrieval periods in comparison with neap conditions.

Turbidity was marginally higher during spring tide with the likelihood of suspended sediments conveyed more readily by advective forces on the spring tide. Chlorophyll-a concentration was low for both tidal regimes however slightly lower during spring tide conditions.

4.1.2 Nutrient results

8 18

6 14

g/L)

10 4 8

Nitrite NO2-N (

Nitrate ( NO3-N 2 4

0 0 Site 1-Neap Site 2-Neap Site 3-Neap Site 2-Spring Site 1-Neap Site 2-Neap Site 3-Neap Site 2-Spring

Sites and tide Sites and tide

10 25

g/L) 8 20

g/L)

6 15

4 10

Total Phosphorus ( Total 2 5

Filterable Reactive Phosphorus (

0 0 Site 1-Neap Site 2-Neap Site 3-Neap Site 2-Spring Site 1-Neap Site 2-Neap Site 3-Neap Site 2-Spring

Sites and tide Sites and tide

220 8

200

180 6

g/L)

g/L) 160

140 4

120

Total Nitrogen ( 100 Ammonia ( NH3-N 2 80

60 0 Site 1-Neap Site 2-Neap Site 3-Neap Site 2-Spring Site 1-Neap Site 2-Neap Site 3-Neap Site 2-Spring

Sites and tide Sites and tide

Figure 5. Typical nutrient concentrations measured for neap and spring tide conditions in Jones Creek.

Nutrient concentrations across both tidal regimes were notably low however soluble fraction nutrients of nitrate and filterable reactive phosphorus were higher during spring tide conditions. Nitrite was measurably low during the spring tide (<1 g/L) in contrast to neap conditions with up to 6.2 g/L measured. Likewise total phosphorus, nitrogen and ammonia concentrations were lower during spring conditions. FRP constituted a reasonably large proportion of the total

9 phosphorus pool over the spring tide. Discrete sampling results, albeit limited, were similar to previous studies (Butler and Padovan, 2005).

4.2 Variability of water quality indicators over tidal cycles

This section presents time-series data for water quality indicators measured in Jones creek for both neap and spring cycles (Fig. 6 -13). Correlations with depth are presented in tables 4 and 5 and further analysis and discussion of variability is presented in hysteresis analysis (Sec 4.3). The median, minimum and maximum for site deployments are presented in the Appendix (Table A2 and Table A3).

Figure 6. Temperature, pH, conductivity and PAR measured at site 1 during neap tide

Figure 7. Dissolved oxygen (corrected), turbidity, chlorophyll fluorescence and PAR measured at site 1 during neap tide.

Figure 8. Temperature, pH, conductivity and PAR measured at site 2 during neap tide.

Figure 9. Dissolved oxygen (corrected), turbidity, chlorophyll fluorescence and PAR measured at site 2 during neap tide.

Figure 10. Temperature, pH, conductivity and PAR measured at site 3 during neap tide.

Figure 11. Dissolved oxygen (corrected), turbidity, chlorophyll fluorescence and PAR measured at site 3 during neap tide.

Figure 12. Temperature, pH, conductivity and PAR measured at site 2 during spring tide.

Figure 13. Dissolved oxygen (corrected), turbidity, chlorophyll fluorescence and PAR measured at site 2 during spring tide.

Table 4. Range of water quality indicators at site 2 during neap and spring tide.

Water quality indicators range

Temperature EC Turbidity DO CF Location pH (°C ) (mS/cm ) (NTU) (%saturation) (µg/L )

Site 2 - neap tide 25.4-26.2 7.9-8.0 53.2-54.1 2.8-7.2 58.9-98.4 0.6-3.3 Site 2 - spring tide* 24.3-25.8 7.9-8.1 53.0-54.6 3.4-11.8 53.1-103.3 0.6-7.1 (* Only one SBE16 instrument was deployed for the spring tide event).

4.2.1 Temperature

Variation in temperature indicates clear temporal patterns. Variation between tidal conditions was minor with temperature ranging between 25.1 and 26.2°C at neap tide (1.2 °C variation) and 24.3 and 25.8°C over the spring tide (1.5 °C variation).

Neap tide temperature tended to increase during day time to reach a peak toward the evening and at low tide. Decreasing trends then persist through the evening with reduced or no sunlight. Similarly spring tide temperature tended to follow comparative patterns.

Temperatures recorded during neap tide are slightly higher than temperatures recorded for spring tide however this is not significant and likely to be associated with longer residence times and reduced mixing associated with neap tidal movement. Overall temperatures measured during the deployments indicate a similar pattern of variation during both tidal settings. Temperature varied over both tidal cycles and with elevations measured more often with the slack of the outgoing tide. Temperature maxima during spring tide events typically occurred at the slack of ebb tide (Fig.12). Temperature is also influenced by the time of the with sunlight maxima peaking around midday and light intensity modulating with diurnal change.

4.2.2 pH pH clearly modulated with tidal cycle indicating clear variation with the neap and spring tidal events examined. pH varied between 7.3 and 8.0 during neap tide and between 7.9 and 8.1 during spring tide (Fig 14 and 15).

On the incoming tide pH increases and on outgoing tides pH decreases albeit within a very narrow range of 0.2 for each site. Correlation coefficients for both neap and spring tides indicated strong positive relationship with tide. This relationship appeared to be more significant during spring conditions (r =0.946).

Changes in pH are similar for both tidal conditions, however temporal variations are more regular with spring tide and indicate strong positive correlations with depth (Table 5). pH varies with tidal cycle for neap and spring tide conditions. Highest values are measured at high tide and lowest values at low tide (Fig. 14 and 15). 19

8.02 8.08

8.06 8.00 8.04 7.98 8.02

7.96 8.00

7.98 7.94

pH pH 7.96

7.92 7.94

7.92 7.90 7.90 7.88 7.88

7.86 7.86 3 4 5 6 7 8 2 3 4 5 6 7 8 9 Depth (m) Depth (m)

Figure 14. pH vs depth during neap cycle (July 2013). Figure 15. pH vs depth spring cycle (Aug 2013).

4.2.3 Electrical conductivity

Changes in electrical conductivity (EC) show a clear tidal pattern. EC varied between 53.1 and 54.5 mS/cm during neap tide and between 53.0 and 54.6 mS/cm over spring tide conditions.

Variation in EC is observed during both tidal cycle conditions. At neap tide, changes in EC are reasonably consistent with the modulation of each tide.

At spring tide, variations of EC appear to more strongly follow tidal cycle variations (r = -0.73). EC was observed to increase with outgoing tides with peaks at top of the tide. Highest values of EC are recorded at the top of the outgoing tide. Modulations were more variable with spring tides with both neap and spring cycles largely remaining representative of marine influence. Variation of EC tended to differ in the extent of change between neap and spring tidal events. At neap tide, EC appears to follow tidal modulation increasing with incoming flood tide. During spring tide incursion EC appears to more strongly follow the tide (Table 5). EC was observed to peak around the slack of the flood tide at each outgoing movement with neap and spring tides. Hysteresis analysis (Sec 4.3) further explores these patterns.

4.2.4 Dissolved oxygen

Changes in dissolved oxygen indicate a temporal pattern with DO varying with tides during both tidal cycle conditions.

DO measured increases and decreases around each high and low tide in addition to reflecting diurnal patterns. During both tidal conditions and at every change of tide (high and low) DO levels tended to decrease. Butler and Padovan (2005) also found similar complex patterns for DO suggesting a number of factors may play a role in determining variability.

Changes in dissolved oxygen indicate a temporal pattern and variations of DO are observed within the tidal cycle for both neap and spring tides. Highest values were measured at high tide 20 and lowest values at low tide. However a decrease in dissolved oxygen is observed at each change of tide (slack of the tide) and typically occurs when mixing is reduced during the change of the incoming and outgoing tides. A more detailed examination of a neap and spring event also indicated clear diurnal changes with time of day another determinant in the variation for dissolved oxygen (Fig. 16 and 17). Dissolved oxygen indicated responses associated with solar radiation inputs with variation (diurnal peaks and troughs) a function of the time of day and dampened by tidal movement, particularly at the top of each tide.

95 8

90 7 85

6 80

75 (m) Depth 5

DO (% Saturation) DO

4 65

60 3

13:00:00 13:15:00 13:30:00 13:45:00 14:00:00 14:15:00 14:30:00 14:45:00 15:00:00 15:15:00 15:30:00 15:45:00 16:00:00 Time

Figure 16. Typical modulation of dissolved oxygen with change in tide and time of day Neap tide – July. ( Dissolved oxygen) and ( - - - depth).

90 10

9 85 8 80 7

75 6

70 5

4 (m) Depth 65 DO (% saturation) (% DO 3 60 2

55 1

50 0

09:22:00 09:32:00 09:42:00 09:51:00 10:01:00 10:11:00 10:21:00 10:31:00 10:41:00 10:51:00 11:00:00 11:10:00 11:20:00 11:30:00 Time

Figure 17. Typical modulation of dissolved oxygen with change in tide and time of day Spring tide– August. ( Dissolved oxygen) and ( - - - depth).

4.2.5 Turbidity

Variation in turbidity appears to be influenced by tidal modulation with neap and spring tides generating turbidity flux along the tidal creek.

At neap tide, changes in turbidity do not appear to significantly change with tide and ranged from 2.2 to 9.1 NTU. However highest values are recorded at low tides and lowest values are recorded at high tide. During neap conditions turbidity was observed to slightly increase with an outgoing tide (Fig.18).

During spring tide conditions turbidity variation indicated strong tidal influence. Turbidity increases on incoming tides and decreases on outgoing tides and varies between 3.4 and 11.8 NTU slightly higher than for neap conditions. Highest values of turbidity are recorded around high tide and lowest values around low tide. However it was observed to decrease at the top of the high tide during slack conditions.

Tidal modulation influences turbidity which also appeared to differ in the degree of variation between spring and neap tidal conditions. Spring tides induced more turbid conditions with highest values at high tide and lowest values at low tide. During neap tidal excursions turbidity does not appear to be as strongly driven by the tide however during spring events a reasonable positive correlation was observed for turbidity (r =0.683). The constrained range of values observed during neap conditions is likely due to dampened tidal velocities limiting mixing and resuspension. During both tidal conditions changes in turbidity also appear to relate to diurnal variations however this may be more aligned with Chla-Fl elevations. Pico-plankton which form a large component of the algal composition (pers. comm. D.Purcell, Australian Institute of Marine Science) could contribute to turbidity in Darwin Harbour.

Turbidity indicated a clear tidal pattern differing between spring and neap tide conditions with a maxima typically observed during spring events. Highest values were recorded at the slack end of an outgoing tide and lowest values at high tide or slack of the tide while current speeds are minimal. The variation of turbidity is greater during spring tide when tidal velocities are stronger. This phenomenon has been observed in previous studies (Padovan, 1997; Wilson et al. 2004). During these cycles tidal mixing and resuspension of sediments in the water column is more pronounced.

Depth (m) Depth 4

3 8

Outgoing tide

Turbidity (NTU) Turbidity

3 05:00:00 09:00:00 13:00:00 17:00:00 Time

Figure 18. Change in turbidity with outgoing tide (Jones Creek July 15, 2013).

4.2.6 Chlorophyll Fluorescence

Changes in chlorophyll fluorescence (CF) indicate a temporal pattern with variations observed within neap and spring tidal conditions (Table 5). CF fluctuated between 0.6 and 3.3 µg/L during the neap tide and between 0.6 and 1.9 µg/L during spring tide conditions. During both tidal cycles highest values of CF were recorded during low tides and lowest values during high tides.

CF was also observed to change with diurnal variation, increasing during day light hours and then declining during the evening. Changes in chlorophyll fluorescence indicate a strong temporal and tidally driven pattern and variations occur over neap and spring tidal cycles.

Table 5. Correlation coefficients (r) for water quality parameters measured versus depth during neap tides. Shaded cells indicate those where good correlation and estimates of r were significant (p <0.05).

Site Parameter r p SB1 Temp -0.108 0.03 pH 0.875 9.68x10-120 -55 EC -0.694 3.39x10

PAR/Irradiance -0.157 0.002

DO %sat 0.130 0.015 -19 Turbidity -0.446 1.0x10 -11 Chla-Fl -0.333 3.96x10 SB2 Temp 0.089 0.085 pH 0.874 1.413x10-118 -32 EC -0.559 3.53x10 PAR/Irradiance 0.0799 0.123 DO %sat 0.228 0.0000857 Turbidity -0.543 4.95x10-30 Chla-Fl -0.392 4.29x10-11 SB3 Temp -0.148 0.0041 pH 0.837 8.2x10-99 EC -0.634 2.9x10-43 PAR/Irradiance -0.0274 0.598 DO %sat 0.0266 0.609 Turbidity -0.726 3.8x10-62 Chla-Fl -0.538 2.46x10-29 ns = not significant

Table 6. Correlation coefficients (r) for water quality parameters measured versus depth during a spring tidal regime. Shaded cells indicate those where good correlation estimates of r were significant (p<0.05).

Site Parameter r p SB2 Temp 0.241 0.00000049 pH 0.946 3.07x10-282 -102 EC -0.743 5.51x10 -41 PAR/Irradiance -0.522 2.0x10 -30 DO %sat 0.450 5.9x10 -80 Turbidity 0.683 3.67x10 -34 Chla-Fl -0.476 8.05x10

4.3 Hysteresis analysis for indicative neap and spring events.

Specific events for neap and spring tide were examined for each water quality parameter against depth yielding 12 hysteresis plots (Fig. 21-22). The parameters examined included water temperature, pH, dissolved oxygen, Chlorophyll-a (FLU), conductivity and turbidity. PAR was omitted given the dependence on sunlight rather than tidal influence.

The neap and spring tide events examined (Fig. 19 and 20) represent a 3 m and a 5.5 m tidal movement respectively for an outgoing (ebb) and incoming (flood) tide.

Figure 19. Neap tide episode examined for hysteresis analysis (shaded). July 18, 2013.

Figure 20. Spring tide episode examined for hysteresis analysis (shaded). August 9, 2013.

The majority of events produced hysteresis loops in a circular (or similar) pattern, highlighting complex behaviours of solutes and tide at different portions of the ebb and flood tide. Generally the type of hysteresis loop generated by the individual events correlated in a predicable manner.

4.3.1 Temperature Temperatures during neap conditions revealed a clockwise pattern with outgoing ebb tide indicating higher water temperatures during neap conditions (Fig. 21a). This pattern was the reverse during spring tides where temperature on the incoming flood tide was higher (Fig. 22a). Differences between temperatures on ebb and flood tides were more marked during spring tide modulation.

4.3.2 pH The neap pH hysteresis plot indicated a clockwise loop with higher pH on incoming waters and lower outgoing conditions (Fig. 21b). An initial peak on the ebb tide may correspond with the typical top of the tide prior to outgoing waters with an outgoing movement. pH variation during the spring tide was slightly larger with higher pH on the incoming flood tide a pattern consistent with incoming marine waters (Fig. 22b).

4.3.3 Conductivity Similarly variation for conductivity was greater during spring tide conditions than that for neap conditions (Fig. 22c). The spring tide hysteresis plot indicated a clockwise pattern with conductivity higher on the flood tide consistent with higher salinity waters entering the tidal creek from the broader harbour. The neap plot implied a counter-clockwise pattern with less variation on the ebb and flood tides (Fig. 21c).

4.3.4 Dissolved oxygen Dissolved oxygen was more closely aligned on the ebb and flood tides during neap conditions (Fig. 21d). A similar anti-clockwise pattern was observed for the spring hysteresis plot (Fig. 22d) with dissolved oxygen decreasing on the outgoing ebb tide and steadily increasing on the flood tide. Differences in dissolved oxygen were greater during spring conditions between the ebb and flood event examined.

4.3.5 Turbidity Turbidity during both events was low maintaining values <11 NTU over the episode examined. The hysteresis plot for spring tide revealed greater variation in turbidity between flood and ebb tide with outgoing ebb tide indicating the highest values decreasing with the outgoing movement (Fig. 22e). Neap hysteresis analysis for turbidity was more complex with a number of minor spikes albeit remaining below 6 NTU for the period observed. Flood and ebb conditions were more closely aligned (Fig. 21e).

4.3.6 Chlorophyll-a Chlorophyll-a remained below 1.5 g/L during the event examined. Neap hysteresis indicated an anti-clockwise pattern with higher concentrations observed on the ebb outgoing tide (Fig. 21f). The flood tide indicated a pattern of increasing concentration with the rising tide, a clear hysteresis loop was observed. The spring tide hysteresis pattern was similar however appeared to reflect a counter clockwise trend. Variance was notably different between ebb and flood episodes (Fig. 22f).

4.3.7 Neap hysteresis plots

8.02

8.00 26.0

C) 25.9

7.98 0

25.8 7.96

25.7 7.94 Temperature (

25.6 7.92

25.5 7.90 4.5 5.0 5.5 6.0 6.5 7.0 4.5 5.0 5.5 6.0 6.5 7.0

Depth (m) Depth (m) a) b)

53.8 75

53.6 70

53.4 65

Conductivity (mS/cm) Conductivity

Dissolved Oxygen sat) (% 53.2 60

53.0 55 4.5 5.0 5.5 6.0 6.5 7.0 4.5 5.0 5.5 6.0 6.5 7.0

Depth (m) Depth (m) c) d)

6.5 1.3

6.0 1.2

5.5 1.1

5.0 1.0

4.5 0.9

Turbidity (NTU)

Chlorophy ll (FLU) 0.8 4.0

0.7 3.5

0.6 3.0 4.5 5.0 5.5 6.0 6.5 7.0 4.5 5.0 5.5 6.0 6.5 7.0 Depth (m) Depth (m) e) f)

Ebb tide (outgoing)

Flood tide (incoming)

Figure 21. Neap tide hysteresis plots for site 2. a) pH, b) Temperature, c) Conductivity, d) Dissolved oxygen, e) Turbidity and f) Chlorophyll.

4.3.8 Spring hysteresis plots

8.08 25.8

8.06 25.6 8.04 25.4 8.02

0 25.2 8.00 (

7.98 pH 25.0

7.96 24.8

7.94 Temperature 24.6 7.92

7.90 24.4

7.88 24.2 2 3 4 5 6 7 8 9 2 3 4 5 6 7 8 9

Depth (m) Depth (m) a) b)

110

53.8 100

53.6 90

53.4 80

Conductiv ity (mS/cm)

Dissolv Oxy ed Sat) (% gen 53.2 70

53.0 60 2 3 4 5 6 7 8 9 2 3 4 5 6 7 8 9

Depth (m) Depth (m) c) d)

12 1.4

1.3 10 1.2

8 1.1

1.0 6

Turbidity (NTU)

Chlorophy ll (FLU) 0.9

4 0.8

2 0.7 2 3 4 5 6 7 8 9 2 3 4 5 6 7 8 9

Depth (m) Depth (m) e) f)

Ebb tide (outgoing)

Flood tide (incoming)

Figure 22. Spring tide hysteresis plots for site 2. a) pH, b) Temperature, c) Conductivity, d) Dissolved oxygen, e) Turbidity and f) Chlorophyll.

Table 7. Synopsis of hysteresis pattern for parameters examined.

Rotational Parameter Tide event Maxima direction

Temperature Neap Anti-clockwise Ebb (0C) Spring Clockwise Flood

Neap Clockwise Top Ebb pH Spring Clockwise Top Flood

Conductivity Neap Anti-clockwise Top Ebb (mS/cm) Spring Clockwise Flood

Dissolved Neap Anti-clockwise Top Ebb oxygen (%Sat) Spring Anti-clockwise Top Ebb

Turbidity Neap Anti-clockwise Top Ebb/Flood (NTU) Spring Anti-clockwise Top Ebb

Top Ebb Chlorophyll-a Neap Anti-clockwise Slack/between Ebb- (FLU) Spring Clockwise Flood

Some indicators, such as pH, electrical conductivity and turbidity, are strongly influenced by tidal conditions. Other indicators (temperature, chlorophyll fluorescence, DO) vary over tidal cycles but also appear to be influenced by other factors. Solar radiation (as PAR) in particular plays a role in variation of temperature and dissolved oxygen in line with diurnal variations.

During neap tide conditions, high tides are associated with a decrease of dissolved oxygen and chlorophyll fluorescence, peaks of turbidity, highest values of pH and lowest values of conductivity. In comparison neap tides or more so the turn of the tide between flood and ebb episodes are associated with lower dissolved oxygen, pH, high electrical conductivity, turbidity and chlorophyll fluorescence values.

Spring tidal conditions at high tides are associated with highest values of pH and lowest values electrical conductivity, lower dissolved oxygen and chlorophyll fluorescence and high values of turbidity. Spring tides typically induce strong tidal currents which produce larger fluctuations in water quality and greater variation.

4.4 Longitudinal variation of water quality along Jones Creek

Longitudinal variation was examined for neap deployments where loggers were located along Jones creek from July 15 to 19, 2013. Loggers were deployed at the creek mouth (Site 1) and extended to site 3, the upper most site (Fig. 2).

Variation around neap tidal conditions for each indicator are presented below (Table 8) and Figure 23 where medians for each indicator are given. Most water quality indicators measured appear to be relatively constant with limited range between sites along the creek.

Changes of temperature are very low between sites and within sites with temperatures tending to increase with distance downstream. pH was slightly higher in the mid-uppermost sites in comparison to the mouth site. This lower pH range at the creek mouth was not expected and may have been due to sensor failure. Discrete measurements for pH (Fig. 4) were similar along the creek albeit limited. During the dry season the Jones Creek system experiences no source of catchment inflows and in conjunction with residence times and continuous ebb and flood tides could result in the persistence of marine waters. However the creek mouth is typically subject to strong marine influence where higher pH would be expected. Conductivity, turbidity and chlorophyll-a indicated similar trends with high medians at the upper most site. The proximity to intertidal and mangrove sediments resuspended with tide may contribute to this spatial pattern in turbidity (Fortune, 2015).

Median DO levels increase with distance from the upper most site consistent with a longitudinal gradient. The observed DO gradient is similar to those observed in other tidal creeks of Darwin Harbour (Butler and Padovan 2005; Fortune, 2015).

Although Chla (FLU) levels recorded are appreciably low during neap conditions a slight increase in the upper reaches was observed (r =-0.538) with a median of 1.1 g/L (Fig. 23).

Changes appear to be reasonably limited for some parameters but an overall longitudinal gradient along the creek was observed. It is likely that the distance between sites along the small tidal creek contribute to the lack of strong concentration gradients.

Table 8. Water quality range parameter at the three sites during neap tide.

Water quality indicators range

Temperature EC Turbidity DO CF Location pH (°C ) (mS/cm ) (NTU) (%saturation) (µg/L )

Site 1 (creek mouth) 25.5-26.2 7.3-7.5* 53.1-54.1 2.2-7.1 58.0-103.3 0.6-1.9 Site 2 (middle) 25.4-26.2 7.9-8.0 53.2-54.1 2.8-7.2 58.9-98.4 0.6-3.3 Site 3 (upper) 25.1-26.2 7.8-7.9 53.2-54.6 2.6-9.1 56.9-95.0 0.6-2.9 *Subject to error given unexpected limited range over deployment.

25.81 8

25.8 7.9 7.8 25.79 7.7

25.78 7.6

25.77 pH 7.5 7.4 25.76

Temperature (oC) Temperature 7.3 25.75 7.2 25.74 7.1 Site 1 (mouth) Site 2 (mid) Site 3 (Upper) Site 1 (mouth) Site 2 (mid) Site 3 (Upper)

a) b)

86 53.74 84

53.72 82 53.7 80 53.68 78 53.66 76 53.64 74 53.62 72 Conductivity (mS/cm) Conductivity 53.6 Dissolved Oxygen sat) (% Oxygen Dissolved 70 53.58 68 Site 1 (mouth) Site 2 (mid) Site 3 (Upper) Site 1 (mouth) Site 2 (mid) Site 3 (Upper)

c) d)

1.11 4.1 4 1.1

3.9

1.09 3.8 1.08 3.7 3.6 1.07 3.5 3.4

1.06 (NTU) Turbidity Chlorophyll (FLU) Chlorophyll 3.3 1.05 3.2 1.04 3.1 Site 1 (mouth) Site 2 (mid) Site 3 (Upper) Site 1 (mouth) Site 2 (mid) Site 3 (Upper)

e) f)

Figure 23. Median values for transect sites 1 to 3, Jones Creek Neap deployment July 2013.

a) Temperature, b) pH, c) Conductivity, d) Dissolved oxygen, e) Chlorophyll and f) Turbidity.

A previous study of the Jones Creek system (Butler and Padovan, 2005) found the similar spatial patterns in water quality. Extensive logging periods and broader spatial sampling design provided improved sensitivity for the assessment of longitudinal trends. It is recommended that future sampling adopt such an approach to better capture neap and spring tide conditions. Ideally sites should be spaced at appropriate distances in order to detect any discernible gradient. However this can be sometimes constrained by suitable access.

5. CONCLUSION

Water quality is influenced by tidal cycle however while tides may influence some parameters others such as water temperature and DO are also influenced solar radiation input and therefore vary as a function of the time of day or a combination of factors.

Given the influence of tide on water quality indicators measured, a monitoring program should take into account the variability due to tidal cycles. In order to limit this variability, water quality monitoring programs undertaken by the Aquatic Health Unit occurs at the same tidal cycle (neap tide) and during a three hour window around high tide, though practical considerations such as undertaking these during business hours limit monitoring opportunities.

Similarly consistency with the time of day for sampling should be considered when undertaking monitoring given the diurnal patterns for some parameters particularly dissolved oxygen.

In order to better understand the temporal variability of Darwin Harbour, the deployment of logger sensors (either on a periodic or permanent basis) at designated monitoring locations is recommended.

Knowledge of the effects of tide on water quality parameters is required when interpreting results over time within the context of guideline compliance. For example, sampling over a tide cycle has demonstrated that in some cases the value of an indicator can fluctuate above and below guideline objectives as a function of tidal stage. Deciphering between the contribution of natural variation with tide and anthropogenic impacts is an important attribute in monitoring programs. Hence where water quality objectives or guidelines may be exceeded, knowledge of the potential influence of tidal stage at sampling will assist in interpreting results.

6. REFERENCES

Brocklehurst, P and Edmeades, B. (1996). The Mangrove Associations of Darwin Harbour. Technical Report No. R96/7. Resource Capability Assessment Branch, Department of Lands, Planning and Environment, Northern Territory Government.

Department of Land Resource Management (2013). Darwin Harbour Region Report Cards. Aquatic Health Unit, Department of Land Resource Management. Darwin, Australia.

Fortune, J. (2015). Spatial variability of Darwin Harbour water quality during dry season neap tides of 2012 and 2013. Report No.16/2015D. Aquatic Health Unit. Department of Land Resource Management. Palmerston, NT.

Mauraud, N. (2013). Darwin Harbour Water Quality: Supplement to the 2013 Darwin Harbour Region Report Card. Report 12/2013D. Aquatic Health Unit, Water Resources Division. Department of Land Resource Management.

Miller, R. L., Bradford, W. L., and Peters, N. E. (1988). Specific Conductance: Theoretical Considerations and Application to Analytical Quality Control. In U.S. Geological Survey Water-Supply Paper.

Padovan, A. (1997). The Water Quality of Darwin Harbour –October 1990 to November 1991. Report No. 34/1997D. Water Quality Branch. Water Resources Division. Dept of Lands Planning and Environment. Palmerston, NT.

Butler, J and Padovan, A. (2005). The water quality of Jones creek, a tidal creek in Darwin Harbour. Report No. 14/2005D. Water Monitoring Branch, Natural Resource Management Division. Department of Natural Resources, Environment and the Arts.

Wilson, D., Padovan, A and Townsend, S. (2004). The water quality of spring and neap tidal cycles in the middle arm of Darwin Harbour. Department Infrastructure, Planning and Environment, Darwin. Photograph: P. Cowan

APPENDIX Table A1: Comparison of dissolved oxygen data.

Dissolved oxygen comparison of data DO DO % Difference Difference Site name Date Time Instrument mg/L % % mg/L Jones Creek 1 15.07.13 1200 Quanta 6.85 102.67 24.09 1.60 15.07.13 12:00 Seabird 7100 5.26 78.58 Jones Creek 2 15.07.13 1245 Quanta 6.77 101.07 4.34 -1.39 15.07.13 12:45 Seabird 7101 8.16 96.73 Jones Creek 3 15.07.13 1345 Quanta 6.67 99.33 30.42 2.08 15.07.13 13:45 Seabird 7102 4.60 68.91 Jones Creek 1 19.07.13 945 Quanta 6.44 95.83 65.08 4.38 19.07.13 9:45 Seabird 7100 2.06 30.75 Jones Creek 2 19.07.13 1015 Quanta 6.58 97.03 49.15 3.38 19.07.13 10:15 Seabird 7101 3.20 47.89 Jones Creek 3 19.07.13 1045 Quanta 7.48 94.03 49.20 4.48 19.07.13 10:45 Seabird 7102 3.01 44.83 Jones Creek 2 09.08.13 910 Quanta 6.49 98.27 22.19 1.33 09.08.13 9:10 Seabird 7101 5.15 76.07 Jones Creek 2 13.08.13 930 Quanta 5.93 90.87 15.87 -0.32 13.08.13 9:30 Seabird 7101 6.24 75.00 Median 27.25 1.84 Average 32.54 1.94 Min 4.34 -1.39

Max 65.08 4.48

Site 1 (Mouth) Site 2 (Mid) 7.5 7.0

7.0 6.5

6.5 6.0

6.0 5.5

5.5 5.0

5.0 4.5

Dissolved oxygen (mg/L) oxygen Dissolved

Dissolved oxygen (mg/L) oxygen Dissolved 4.5 4.0

4.0 3.5 15/07/13 16/07/13 17/07/13 18/07/13 19/07/13 20/07/13 15/07/2013 16/07/2013 17/07/2013 18/07/2013 19/07/2013 20/07/2013

Date Date

Figure A1. Corrected dissolved oxygen for site 1 (Mouth) neap tide. Figure A2. Corrected dissolved oxygen for site 2 (Mid) neap tide.

Site 3 (Upper) Site 2 (Mid)

7.0 7.5

6.5 7.0

6.0 6.5

6.0 5.5

5.5 5.0 5.0 4.5 4.5

Dissolved oxygen (mg/L) oxygen Dissolved 4.0 (mg/L) oxygen Dissolved 4.0 3.5 3.5 15/07/13 16/07/13 17/07/13 18/07/13 19/07/13 20/07/13 09/08/13 10/08/13 11/08/13 12/08/13 13/08/13 14/08/13 Date Date

Figure A3. Corrected dissolved oxygen for site 3 (Upper) neap tide. Figure A4. Corrected dissolved oxygen for site 2 (Mid) spring tide.

Table A2: Median, minimum and maximum for neap tide conditions

Parameter Site Median Min Max Temperature Site 1 25.8 25.48 26.21 Site 2 25.8 25.41 26.21 Site 3 25.76 25.13 26.21 Conductivity Site 1 53.64 53.14 54.1 Site 2 53.65 53.18 54.12 Site 3 53.73 53.2 54.46 pH Site 1 7.4 7.33 7.45 Site 2 7.94 7.88 8.09 Site 3 7.88 7.79 7.97 DO (%sat) Site 1 83.96 58.01 103.3 Site 2 76.33 58.87 98.37 Site 3 73.91 56.94 95.03 Chla (FLU) Site 1 1.06 0.64 1.9 Site 2 1.09 0.61 1.73 Site 3 1.1 0.61 2.89 Turbidity (NTU) Site 1 3.4 2.19 7.09 Site 2 4 2.8 7.1 Site 3 3.9 2.6 9.1

Table A3: Median, minimum and maximum for spring tide conditions

Parameter Site Median Min Max Temperature Site 2 25.15 24.33 25.76 Conductivity Site 2 53.64 53.09 54.57 pH Site 2 7.98 7.87 8.05 DO (%sat) Site 2 69.26 53.08 101.6 Chla (FLU) Site 2 1.08 0.76 1.88 Turbidity (NTU) Site 2 5.6 3.4 11.8