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Summary: Millions of native fish are entrained into irrigation pumps in Australian rivers every year. It is often assumed these fish are wild, but stocked fish may also be affected. During fish entrainment surveys at two pump intakes on the Macquarie River, New South Wales, a noticeable increase of entrained juvenile Murray Cod (Maccullochella peelii) was observed. DNA parentage analysis confirmed that a large proportion of these fish were linked to nearby fish restocking events. At both pump intakes, genetic analysis confirmed that at least 70% and 17% of the individuals sampled were stocked fish. This equated to up to 3% of the fish that were stocked – most of which were entrained less than 24 h after their release. Given the large number of unscreened irrigation pumps in this reach of river, and more broadly throughout the Murray–Darling Basin, fish losses at pump intakes have the potential to remove large numbers of stocked fish from the river where they are released to support native fish recovery and boost recreational fishing opportunities. The use of fish‐protection screens at pump intakes may be a suitable solution to reduce the number of fish entrained and thus increase the survival of recently stocked fish in the rivers. [ABSTRACT FROM AUTHOR]

Context: Rapid human population growth has increased demand for water supply, food security, electricity, and flood mitigation worldwide. To address these challenges, governments have invested heavily in the expansion of water infrastructure. However, there is substantial evidence that globally, this infrastructure impacts aquatic ecosystems and can have a significant impact on the persistence of fish species. Despite being well understood globally, the impacts of dams on fish have been given scant attention in Indonesia. Thus, considerations for fish are rarely included in river development planning frameworks. Methods: To document the impact of riverine barriers on Indonesian freshwater fish, we surveyed multiple sites, using three different kinds of gear (gillnets, castnets, and bait traps), upstream and downstream of Perjaya Dam in the Komering River. Key results: The study revealed 13 of 36 species were found only downstream of the dam and five of 36 species were found only above the dam. There were significant differences in fish community composition between upstream and downstream regions using either fish abundance (Pseudo- F = 4.495, d.f. = 1, P < 0.05), species richness (Pseudo- F = 15.837, d.f. = 1, P < 0.05) or species diversity as the response metrics (Pseudo- F = 8.3256, d.f. = 1, P < 0.05). Conclusions: The local extirpation of many species from upstream areas suggests that the Perjaya Dam hinders fish migration. Implications: Despite containing a fishway, the results indicate that fish are not successfully recolonising upstream reaches. Dams are known to impact fish community structure, however, the impacts of dams on the fish community in Indonesia is understudied. We sampled the fish community upstream and downstream of a dam fitted with a fishway, identifying significant differences in fish community structure. This highlights the need for further research into the operation of the dam, and fishway, to improve fish passage success. [ABSTRACT FROM AUTHOR]

Context: The ability to accurately assess biodiversity is a critical first step towards effective conservation and management. However, assessment of biodiversity using conventional monitoring programs is often constrained by high cost and a lack of taxonomic expertise. Environmental DNA (eDNA) metabarcoding may be a useful tool to efficiently catalogue biodiversity in areas that cannot be easily assessed using other methods. Aims: Here, we evaluated the potential of eDNA metabarcoding for assessing fish biodiversity and distribution in the Kumbe River, Papua Province, Indonesia. Methods: We selected four sampling locations and collected seven eDNA samples from each location. We used eDNA metabarcoding of the Cytochrome- b gene to characterise the fish community. Key results: A total of 23 species were detected, three of which comprised 92% of sequence reads detected: Melanotaenia goldiei (32%), Craterocephalus randi (31%), and the invasive tilapia Oreochromis niloticus (29%). Only five species that were previously detected using conventional methods were detected by metabarcoding: M. goldiei , Craterocephalus stercusmuscarum , O. niloticus , Neoarius graeffei , and Arius arius. We detected 18 species (70% native) that have never been recorded from the Kumbe River. Conclusions: This work has demonstrated that fish biodiversity is substantially underestimated in the Kumbe River. Environmental DNA metabarcoding is a promising rapid, non-invasive and cost-effective method for assessing fish biodiversity in Papua. Implications: The findings support future investment in eDNA metabarcoding to characterise the fish biodiversity in Papua. This will assist in allocating the limited resources for conservation and management to areas most at risk from anthropogenic impacts. Environmental DNA (eDNA) metabarcoding shows great promise as a novel tool for fish biomonitoring programs in tropical freshwater habitats. It is sensitive, non-invasive and cost-effective. However, our results highlight that eDNA metabarcoding cannot be routinely applied without further research into sampling design, marker choice, seasonal data, and an improved reference database to reduce false negative detections. Despite this, eDNA metabarcoding will play an important role in the future characterisation of the fish community in tropical river systems. [ABSTRACT FROM AUTHOR]

Diadromous fishes, those that migrate between fresh and marine waters, are among the most vulnerable species to river infrastructural development. These fish need to move between fresh water and the sea, so any obstruction to migration can block access to critical habitat areas. The Lower Mekong Basin (LMB) is experiencing an unprecedented boom in river development, with many dams and irrigation schemes being installed. Although general patterns of fish migration are known in the LMB, there is relatively little information on diadromous fish migration, so the overall impacts of river development on their population status is likely underestimated for many species. In this study, we reviewed the available information for over one thousand Mekong fish species to identify evidence for diadromy. Our results found that diadromy is likely a more common life history trait in the LMB than previously assumed. For instance, 61 of the 1136 Mekong fish species assessed exhibit diadromous traits (44 amphidromous species, 9 anadromous species, and 8 catadromous species). Many of these species are known to migrate relatively long distances, connecting with the Mekong estuary to some extent to complete their life cycles. Based on routine fish catch monitoring data, these suspected diadromous fishes contributed around 3% to the total catch across the basin and included a number of endemic species of significant economic value. Riverine development must therefore proceed in a balanced manner to protect diadromous species diversity and associated fisheries resources, whilst also meeting food and energy demands in the region. [ABSTRACT FROM AUTHOR]