1. The influence of hydraulic conditions on the spatial distribution of macroinvertebrate assemblages was investigated in three riffles in a perennial Australian river. 2. Velocity, depth and variability of substrate roughness were measured at each of 56 macroinvertebrate sampling locations. Complex hydraulic variables (roughness Reynolds number, shear velocity, Froude number) were calculated from combinations of two or three of the directly measured variables. The biological significance of directly measured and complex hydraulic variables was determined by a combination of univariate and multivariate statistical procedures. 3. Macroinvertebrate abundance, number of taxa and community composition were significantly different between the identified roughness Reynolds number, Froude number, velocity and shear velocity microhabitats throughout the studied riffles. 4. Regression analysis showed macroinvertebrate abundance and number of taxa were negatively related to roughness Reynolds number, shear velocity, velocity and Froude number. Depth was negatively related to abundance. In general, the majority of the macroinvertebrate community preferred the areas of riffles with the lowest near-bed turbulence. 5. Roughness Reynolds number explained more of the spatial variation in invertebrate abundance, number of taxa and community composition than the other hydraulic variables, either directly measured or calculated. Of the directly measured variables, velocity had the greatest explanatory power, which was marginally less than roughness Reynolds number and shear velocity. 6. This study demonstrated that small-scale differences in hydraulic conditions created by combinations of velocity, depth and substrate roughness have an important role in the spatial distribution of macroinvertebrate assemblages in riffle habitats.

Proposed environmental flow regime changes downstream of a major water supply dam have been assessed in terms of effects on depth, velocity and fish passage across natural, gravel-bed riffles and rapids. This study focussed on passage requirements for Australian bass, Macquaria novemaculeata (Perciformes, Percichthyidae), a catadromous fish of considerable ecological and recreational fishing importance. Some 23 major riffles and rapids occur between the dam and the tidal limit over a river length of 25 km. Reconnaissance investigations of riffle slope, length, width, depth and morphologic characteristics indicated that wideshallow, steep-turbulent and bifurcating riffle morphologies were most likely to cause problems for upstream bass passage under low flow conditions. Two approaches were used to investigate riffle depths and velocities over a range of flows. A rapid assessment approach directly measured thalweg depths and velocities under two controlled flow release rates in riffles identified as being potentially problematic to upstream bass passage. Detailed topographic surveys and two dimensional hydraulic modelling with River2D was undertaken for two riffles identified as 'worst case' examples of wide-shallow and steep-turbulent morphologies. Results from both approaches were consistent and complementary. Both approaches identified riffles where minimum depths and maximum velocities were likely to be problematic for upstream passage by Australian bass at a flow rate of 130 MLd À1 (the current regulated flow release) but were mitigated at flow rates above 300 MLd À1. Assessment of environmental flow regime transparency and translucency threshold options with regard to a 300 MLd À1 target flow indicated that options where the transparency threshold was set at the 80th flow duration percentile (flows equalled or exceeded for 80% of time), and varied according to the monthly pattern of natural flows, improved hydraulic conditions for upstream bass migration.

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The presence of threatened or endangered species often strongly influences management and conservation decisions. Within the Murray–Darling Basin (MDB), Australia, the presence of threatened native fish affects the management and allocation of water resources. In New South Wales, these decisions are currently based on traditional fisheries data and a predictive MaxEnt model. However, it is important to verify the model's predictive power given the implication it may have, but this requires methods with a high detection sensitivity for rare species. Although the use of environmental DNA (eDNA) monitoring, in particular eDNA metabarcoding, achieves a higher detection sensitivity compared with traditional methods, earlier surveys in the MDB have shown that the highly abundant and invasive common carp (Cyprinus carpio) can reduce detection probabilities for rare species. Consequently, a polymerase chain reaction (PCR) blocking primer designed to block the amplification of carp eDNA could increase the detection probabilities for rare native species while simultaneously reducing the required sampling effort and survey costs. Although PCR blocking primers are often used in ancient DNA and dietary studies, no aquatic eDNA metabarcoding study to date has evaluated the potential benefits of using PCR blocking primers. A laboratory and field‐based pilot study was used to address this knowledge gap and assess the impact of a blocking primer, targeting cyprinid fishes (including carp), on the detection probabilities of native species and the minimum sampling effort required. Results showed that the inclusion of the blocking primer increased the detection probabilities for native species by 10–20% and reduced the minimum required sampling effort by 25–50%. These findings provide important insights into possible methods for optimizing eDNA metabarcoding surveys for the detection of rare aquatic species.