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Freshwater Ecosystems—Biodiversity and Protection: 2nd Edition
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Freshwater Ecosystems—Biodiversity and Protection: 2nd Edition

A special issue of Water (ISSN 2073-4441). This special issue belongs to the section "Biodiversity and Functionality of Aquatic Ecosystems".

Deadline for manuscript submissions: 20 July 2026 | Viewed by 8089

Special Issue Editors

Dr. Dubravka Čerba

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Guest Editor
Department of Assessment and Aquatic Ecosystems Research, National Water Reference Laboratory of Slovakia, Water Research Institute, Bratislava, Slovakia
Interests: Chironomidae; macrozoobenthos; epiphyton; hydrobiology; water quality assessment; freshwater biodiversity; paleolimnology
Special Issues, Collections and Topics in MDPI journals
Dr. Filip Stević

E-Mail Website
Guest Editor
Department of Biology, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
Interests: aquatic ecology; phytoplankton taxonomy and ecology; phytoplankton functional groups; floodplain ecology; invasive species; water quality assessment
Special Issues, Collections and Topics in MDPI journals
Dr. Maja Raković

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Guest Editor
Institute for Biological Research "Siniša Stanković" National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
Interests: freshwater Mollusca (Gastropoda and Bivalvia); macroinvertebrates; taxonomy and population genetics; water quality assessment; invasive species

Special Issue Information

Dear Colleagues,

There are currently a number of concerns in all ecosystems regarding biodiversity and habitat protection. This is especially true for freshwater ecosystems, since some of the strongest negative anthropogenic influences are evident in the lakes, rivers, ponds, and floodplains in our vicinity. Globally, there is an ongoing struggle with the challenges of protecting biodiversity; decreasing habitat destruction; ensuring vital ecological services; and developing various methods to actively assess and monitor aquatic habitats (and communities) as well as plans and models for the protection, revitalization, and restoration of natural freshwater ecosystems. To achieve these goals, it is vital to understand how such systems function, the status of the communities present, and the main influencing factors at play. Furthermore, the application of biotic elements or multi-indicator methods can be helpful in the protection and management of the studied freshwater system.

The aim of this Special Issue is to present reviews, notes, and original research that concern the following issues: diversity studies of various types of freshwater ecosystems, water quality assessment methods and application, important stressors in lentic and lotic ecosystems, biodiversity in human-made water bodies, bioassessment of natural and human-made water bodies, main anthropogenic influences in freshwater ecosystems, community structure and functional complexity (from plankton to benthos), and applications of eDNA analysis and molecular taxonomy.

We believe these subjects will be of significant aid for the further development of biodiversity studies as well as in the monitoring and protection of freshwater ecosystems.

Dr. Dubravka Čerba
Dr. Filip Stević
Dr. Maja Raković
Guest Editors

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Water is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • freshwater communities
  • α, β, γ diversity
  • biotic indicators
  • water quality assessment
  • anthropogenic influence
  • ecotoxicology
  • metacommunity
  • invasive species
  • non-wadeable rivers
  • conservation
  • barcoding

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Published Papers (6 papers)

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Research

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24 pages, 2993 KB  
Article
Tributary-to-Mainstream Aquatic Macroinvertebrate Discontinuities in the Colorado River, Southwestern USA
by Lawrence E. Stevens, Joseph H. Holway and Craig Ellsworth
Water 2026, 18(3), 395; https://doi.org/10.3390/w18030395 - 3 Feb 2026
Viewed by 696
Abstract
Tributary-to-mainstem discontinuities (TMDs) are understudied, but are likely common in river networks, arising from abrupt transitions in stream order and dominant ecological factors. We present a conceptual model of aquatic macroinvertebrate (AMI) TMD directionality and relative magnitude by contrasting the impacts of hydrography, [...] Read more.
Tributary-to-mainstem discontinuities (TMDs) are understudied, but are likely common in river networks, arising from abrupt transitions in stream order and dominant ecological factors. We present a conceptual model of aquatic macroinvertebrate (AMI) TMD directionality and relative magnitude by contrasting the impacts of hydrography, geochemistry, and sediment transport on tributary-related channel-floor precipitate cementation and the mainstream embeddedness (burial) of channel-floor substrata in fine sediment. We test that model using AMI assemblage density/m2, species richness/sample, and diversity data from 24 tributaries confluent with the regulated Colorado River in Grand Canyon through pairwise and multivariate analyses of long-term discharge records and substrate and water-quality data in three habitats: tributaries, their confluences, and adjacent mainstream habitats. Mean AMI density decreased 2.7-fold from low to high cementation, 6.1-fold from low-to-high embeddedness, and 136.0-fold across combined gradients. We also analyzed pre-dam aquatic insect literature, finding that TMDs were naturally common in Glen Canyon upstream but were more strongly tributary-positive (discontinuity magnitude, Dmag = 0.62 in pre-dam Glen Canyon) compared to tributaries in the post-dam Grand Canyon (Dmag = 0.31). We conclude that, depending on Dmag directionality, tributary confluences can function as hotspots or barriers to AMI assemblage development. Our results demonstrate that TMDs are and were common in the contemporary regulated and natural unregulated Colorado River corridor, and we expand the concept of biotic discontinuity to improve understanding of fluvial ecosystem ecology and constraints on river and dam management. Full article
(This article belongs to the Special Issue Freshwater Ecosystems—Biodiversity and Protection: 2nd Edition)
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20 pages, 6204 KB  
Article
Integrating Spatial, Bioclimatic, and Biotic Predictors of Ostracod Diversity Across Botswana’s Inland Waters
by Agata Szwarc and Tadeusz Namiotko
Water 2026, 18(1), 46; https://doi.org/10.3390/w18010046 - 23 Dec 2025
Viewed by 890
Abstract
Understanding the factors that structure freshwater invertebrate assemblages is essential for predicting biodiversity patterns across heterogeneous landscapes. Here, we provide the first comprehensive assessment of ostracod diversity across multiple freshwater ecoregions of Botswana, a semi-arid country encompassing a wide range of hydrological and [...] Read more.
Understanding the factors that structure freshwater invertebrate assemblages is essential for predicting biodiversity patterns across heterogeneous landscapes. Here, we provide the first comprehensive assessment of ostracod diversity across multiple freshwater ecoregions of Botswana, a semi-arid country encompassing a wide range of hydrological and climatic conditions. We analyzed ostracod assemblages from 19 sites, integrating spatial, regional, and local environmental variables with biotic predictors derived from macro-, meio-, and microinvertebrate communities. Multivariate analyses revealed that spatial variables, strongly correlated with bioclimatic gradients, were the dominant predictors of ostracod assemblage composition. These gradients reflected broad-scale climatic differences among ecoregions and explained substantially more variation than local physical and chemical water properties. Biotic interactions, represented by taxonomic and functional composition of associated invertebrates and vegetation type, also significantly contributed to model performance, highlighting their previously underappreciated role in shaping ostracod assemblages. Local abiotic environmental factors had comparatively weak explanatory power. Our findings demonstrate that ostracod diversity in Botswana is primarily structured by large-scale spatial–bioclimatic patterns, with additional influence from biotic interactions. This study provides new insights into the ecological drivers of freshwater microcrustaceans in semi-arid regions and establishes a baseline for future biodiversity assessments in southern Africa. Full article
(This article belongs to the Special Issue Freshwater Ecosystems—Biodiversity and Protection: 2nd Edition)
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14 pages, 1733 KB  
Article
Occurrence and Seasonal Variation of Picoplankton at Saiysad Freshwater in Taif City, Saudi Arabia
by Najwa Al-Otaibi
Water 2025, 17(18), 2788; https://doi.org/10.3390/w17182788 - 22 Sep 2025
Viewed by 1001
Abstract
A wadi ecosystem, a wetland characterized by seasonal water flow, is a unique freshwater environment typically found in semi-arid and arid regions. This study investigates the seasonal and spatial dynamics of environmental properties and microbial plankton communities at Wadi Saiysad in Taif City, [...] Read more.
A wadi ecosystem, a wetland characterized by seasonal water flow, is a unique freshwater environment typically found in semi-arid and arid regions. This study investigates the seasonal and spatial dynamics of environmental properties and microbial plankton communities at Wadi Saiysad in Taif City, Saudi Arabia. Using flow cytometry, three distinct picoplankton populations were observed: Synechococcus and heterotrophic prokaryotes classified as low (LNA) or high (HNA) nucleic acid content. Surface freshwater samples were collected from three distinct sites, representing habitats with actively flowing water, biodiverse communities, and human-influenced areas. Interestingly, no significant differences among stations were observed, suggesting that the sampled stretch of Wadi Saiysad receives similar nutrient inputs. Seasonal water temperature reached 24.5 ± 0.57 °C in summer and the pH ranged from neutral to slightly alkaline. Nutrient analyses revealed that Wadi Saiysad is eutrophic and limited by phosphorus. Phytoplankton biomass was dominated by nanoplankton, particularly in summer (46.60 ± 5.33%), while Synechococcus increased significantly with a maximum abundance of 1.32 × 104 cells mL−1 during the cooler months. HNA prokaryotes displayed marked seasonal variation (1.95 × 104–1.78 × 105 cells mL−1) compared to LNA prokaryotes (2.05–8.17 × 104 cells mL−1). This study highlights the urgent need for monitoring and managing the nutrient inputs in Wadi Saiysad to protect its biodiversity and support sustainable use. Full article
(This article belongs to the Special Issue Freshwater Ecosystems—Biodiversity and Protection: 2nd Edition)
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19 pages, 2931 KB  
Article
Integrating Microbial Source Tracking to Unravel Impacts of Wastewater Discharge on Spatial Distribution of Riverine Microbial Community
by Yanru Fan, Hongbin Gao, Zhongfeng Jiang, Yuran Lv, Xiang Guo, Xinfeng Zhu, Junfeng Wu, Yizhe Li, Wenxiang Yu, Qi Li and Keyu Yuan
Water 2025, 17(18), 2753; https://doi.org/10.3390/w17182753 - 17 Sep 2025
Cited by 1 | Viewed by 1210
Abstract
Microbial communities play a pivotal role in material cycling, energy flow, and pollutant degradation within river ecosystems. Thus, gaining a clear understanding of how wastewater discharge affects microbial community structure and function is essential for the protection and management of the surface water [...] Read more.
Microbial communities play a pivotal role in material cycling, energy flow, and pollutant degradation within river ecosystems. Thus, gaining a clear understanding of how wastewater discharge affects microbial community structure and function is essential for the protection and management of the surface water environment. In this study, a total of 9 samples were collected from the Sha River in March 2024. Subsequently, 16S rRNA sequencing technology combined with investigation of physicochemical properties of water was used to investigate the compositional diversity, spatial distribution, and explore the environmental effects of wastewater discharged on microorganisms. The sequencing results of species at the phylum level revealed that the dominant microbial phyla in the Sha River were primarily Proteobacteria (55.4%), Actinobacteriota (24.0%), Bacteroidota (14.3%), and Verrucomicrobiota (2.6%). The most dominant phylum, Proteobacteria, exhibited varying abundances across different sampling sites in the Sha River basin, with the highest abundances observed at Sites S2, S4, S5, and S6. This is mainly due to the fact that the upstream areas of Sites S2, S4, S5, and S6 are characterized by high concentrations of COD and NH3-N, which are caused by wastewater discharge. Quantitative analysis was also conducted using the Source Tracker model; the results showed that S2 (36.7%) and S4 (31.3%) in the upper reaches of the Sha River are the primary contributors to the microbial community in the downstream catchment area (S6). The study found that the impact of wastewater discharge on the microbial community in the downstream water body exhibits a “longitudinal persistence of microbial signatures” even though the physicochemical pollution indicators of the water body have decreased. These findings of this study represent the application in microbial source tracking in the upstream and downstream sections of rivers, providing strong support for formulating more effective environmental protection strategies in the Sha River basin. Full article
(This article belongs to the Special Issue Freshwater Ecosystems—Biodiversity and Protection: 2nd Edition)
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16 pages, 3525 KB  
Article
A Decade of Change in the Floodplain Lake: Does Zooplankton Yield or Resist?
by Anita Galir, Filip Stević, Karla Čmelar, Dubravka Špoljarić Maronić, Tanja Žuna Pfeiffer and Nikolina Bek
Water 2025, 17(17), 2638; https://doi.org/10.3390/w17172638 - 6 Sep 2025
Cited by 1 | Viewed by 1531
Abstract
Natural ecosystems, especially those regulated by floods, are sensitive to prolonged temperature fluctuations that affect hydrology and the lateral connection between the river and its floodplain. Here, we analyzed a series of zooplankton data collected monthly from 2007 to 2016 during the ice-free [...] Read more.
Natural ecosystems, especially those regulated by floods, are sensitive to prolonged temperature fluctuations that affect hydrology and the lateral connection between the river and its floodplain. Here, we analyzed a series of zooplankton data collected monthly from 2007 to 2016 during the ice-free period in Kopački Rit Nature Park in the Middle Danube, an area important as a food source and nursery area for fish stocks in the Danube. The aim was to find out how the long-term change in temperature and fluctuating environmental parameters affect the succession of zooplankton in the warmer (from April to September) and colder parts of the year (from October to March). Throughout the decade, total nitrogen concentrations showed significant differences between years, with an increase since 2012. Despite the increase in nitrogen levels and the expected increase in primary production, the higher nitrogen levels were accompanied by lower zooplankton biomass. A significant difference was found between the values of the zooplankton geometric mean index, with 73% of the variance explained by the difference between groups. In general, a trend toward a significant decrease in zooplankton biomass, with a simultaneous increase in the number of species and high turnover rates, was observed throughout the decade. Full article
(This article belongs to the Special Issue Freshwater Ecosystems—Biodiversity and Protection: 2nd Edition)
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Review

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11 pages, 1806 KB  
Review
Invasive Crayfish Stepping as a Potential Threat for Coastal Waters
by Massimiliano Scalici and Luca Gallitelli
Water 2025, 17(10), 1519; https://doi.org/10.3390/w17101519 - 17 May 2025
Viewed by 1567
Abstract
Species belonging to the crustacean infraorder Astacoidea represent taxa of particular interest from a conservation point of view, such as the threatened European crayfish (i.e., Austropotamobius pallipes), and at the same time include invasive taxa having highly negative impacts where they are [...] Read more.
Species belonging to the crustacean infraorder Astacoidea represent taxa of particular interest from a conservation point of view, such as the threatened European crayfish (i.e., Austropotamobius pallipes), and at the same time include invasive taxa having highly negative impacts where they are introduced. Among the latter, some freshwater-dwelling species seem to show some abilities to tolerate high salinity levels, such as Procambarus clarkii Girard, 1852. By using metadata and field observation, this review will investigate whether the alien P. clarkii can threaten coastal waters. Specifically, we will shed light on P. clarkii’s (1) invasiveness, (2) its dispersal pattern, (3) its tolerance to salinity, and (4) its ecological plasticity as an invasive species in relation to estuaries. This new habitat colonization is also possible as P. clarkii has been observed to survive up to 20 ppt of water salinity and a maximum of 30–35 ppt with its lifetime drastically reduced. As a result, P. clarkii colonizes different ecosystems globally, reaching estuarine and coastal ecosystems due to active and passive transport by human and animal vectors. Due to recent discoveries of alien crayfish in estuarine and coastal waters, monitoring activities have become mandatory to preserve coastal habitats and all the aquatic resources (e.g., limicolous birds, endemic fish, fishery and aquaculture activities) inhabiting therein. Full article
(This article belongs to the Special Issue Freshwater Ecosystems—Biodiversity and Protection: 2nd Edition)
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