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Figure S1. Occurrence of in-stream habitats as a proportion of total habitat per site. Note: bars may not reach 100% as only sampled habitats (and dry streambed) are included in figure. Site codes represent river: BA, Basalt River; C, Cape-Campaspe River; BU, Burdekin River; K, Keelbottom Creek.

Figure S2. Temporal change of secchi depth, periphyton cover and leaf litter cover in edge habitats by site. Benthic leaf litter and periphyton cover were quantified using a percentage score (0 = <10% cover, 1 = 10-35%, 2 = 35-65%, 3 = 65-90%, 4 = > 90%). Edge habitat not present in sites BA1, BA2, K1, and K2 due to encroachment of aquatic macrophytes. Numbers in figures indicate sampling times (1, May 2008; 2, July 2008; 3, October 2008; 4, December 2008a; 5, December 2008b; 9, May 2009). Letters in site codes indicate river as per Figure S1.

Figure S3. Temporal change in log10abundance for key taxa in sandy pools. Bars represent five samplingtimes (L to R: May, July, October, and December 2008; May 2009).Site codes represent river as in Figure S1. “0” = zero count.

Figure S4. Temporal change in log abundance forkey taxa from edge (E) and run (RU) habitats. Bars represent fivesampling times (L to R: May, July, October, and December 2008; May2009). Site codes represent river as in Figure S1. “0”= zero count, “n” = no sample.

Figure S5. Temporal change in richness at the site level for macroinvertebrate assemblages from the edge habitat. Sampling times as per Figure S2, letters in site codes indicate river as per Figure S1.

Figure S6. Temporal change in richness at thesite level for macroinvertebrate assemblages from the sandy pool(SP) and run (RU) habitats. Sampling times as per FigureS2. letters in site codes indicate river as per Figure S1.

Table S1. Significant indicator values (IndValue) for Burdekin macroinvertebrates using theDufrêne-Legendre (1997) method with a Monte Carlo test.Values organised according to a priori groupings of habitat andsorted by Indicator Value.

Table S2. Relationships between themacroinvertebrate assemblage matrix and temperature as indicated bythe RELATE routine in PRIMER. n is the number of samples(i.e. months), ρ is the test statistic, and P isthe probability value. Sig. indicates significance level ofP.

Table S3. Summary of taxa with significantcorrelations (Pearson’s r, p < 0.01) with the dominant NMS axes (% variance explained) of ordinations by site and habitat across all times. Blank fields indicate taxa not found in sample, boldface indicates highest value per habitat.

Table S4. Correlation (Pearson’sr) of edge habitat macroinvertebrates with strongest (%variance) NMS axes by site across all times. Significant (P< 0.01) r-values shown in boldface.

Table S5. Correlation (Pearson’sr) of sandy pool macroinvertebrates with strongest (%variance) NMS axes by site across all times. Significant (P< 0.01) r-values shown in boldface.

Table S6. Correlation (Pearson’sr) of run habitat macroinvertebrates with strongest (%variance) NMS axes by site across all times. Significant (P< 0.01) r-values shown in boldface.

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