When the regime of a river is not perennial, there are four main difficulties with the use of hydrographs for assessing hydrological alteration: i) the main hydrological features relevant for biological communities are not quantitative (discharges) but qualitative (phases such as flowing water, stagnant pools or lack of surface water), ii) stream flow records do not inform on the temporal occurrence of stagnant pools, iii) as most of the temporary streams are ungauged, their regime has to be evaluated by alternative methods such as remote sensing or citizen science, and iv) the biological quality assessment of the ecological status of a temporary stream must follow a sampling schedule and references adapted to the flow- pool-dry regime. To overcome these challenges within an operational approach, the freely available software tool TREHS has been developed within the EU LIFE TRIVERS project. This software permits the input of information from flow simulations obtained with any rainfall-runoff model (to set an unimpacted reference stream regime) and compares this with the information obtained from flow gauging records (if available) and interviews with local people, as well as instantaneous observations by individuals and interpretation of ground-level or aerial photographs. Up to six metrics defining the permanence of water flow, the presence of stagnant pools and their temporal patterns of occurrence are used to determine natural and observed river regimes and to assess the degree of hydrological alteration. A new regime classification specifically designed for temporary rivers was developed using the metrics that measure the relative permanence of the three main phases: flow, disconnected pools and dry stream bed. Finally, the software characterizes the differences between the natural and actual regimes, diagnoses the hydrological status (degree of hydrological alteration), assesses the significance and robustness of the diagnosis and recommends the best periods for biological quality samplings.

Comprehensive knowledge of the effects of disturbances on biodiversity is crucial for conservation and management, not least because ecosystems with low biodiversity may be the most vulnerable. In rivers, the role of disturbance in shaping aquatic biodiversity has mainly focused on floods. Perennial rivers (PRs) often flood, whereas intermittent rivers (IRs) flood, stop flowing and dry. Despite the recent and significant increase in research on IRs, controversy remains about whether they are more or less biodiverse than PRs. Our aim was to determine (Q1) if PRs and IRs differ in biodiversity and (Q2) if the direction and magnitude of the differences (effect sizes) are related to environmental (climate, season, habitat, longitudinal zonation and anthropogenic disturbance) and/or biological factors (taxonomic group). We conducted a meta‐analysis on 44 published studies of PR and IR biodiversity that had replicated data. We applied random effects models to the data to obtain weighted mean effect sizes for differences between PRs and IRs, and their confidence intervals, by first considering all studies and then by splitting studies into groups on the basis of the above factors. We found that biodiversity was significantly higher in PRs than in IRs (Q1). We also detected significant differences (PRs> IRs) in studies of macroinvertebrates, in those conducted within arid and temperate climates, dry and wet sampling seasons, headwaters, and regions subject to different levels of anthropogenic disturbance (Q2). Our meta‐analysis suggests that the expected increase in the prevalence of IRs in certain regions of the world due to global change could result in a decrease in freshwater biodiversity. To better manage and preserve aquatic biodiversity under future global change scenarios and to avoid potential ecosystem consequences of biodiversity loss, conservation efforts should be targeted towards those environmental conditions or taxonomic groups with significant differences (PRs > IRs).

Temporary rivers are characterized by shifting habitats between flowing, isolated pools, and dry phases. Despite the fact that temporary rivers are currently receiving increasing attention by researchers and managers, the isolated pools phase has been largely disregarded. However, isolated pools in temporary rivers are transitional habitats of major ecological relevance as they support aquatic ecosystems during no-flow periods, and can act as refugees for maintaining local and regional freshwater biodiversity. Pool characteristics such as surface water permanence and size, presence of predators, local physicochemical conditions, time since disconnection from the river flow, or distance to other freshwater habitats challenge a comprehensive understanding of the ecology of these habitats, and challenge ecological quality assessments and conservation practices in temporary rivers. In this paper, we aim at providing a characterization of isolated pools from a hydrological, geomorphological, physicochemical, biogeochemical, and biological point of view as a framework to better conceptualize, conserve, and manage these habitats.

1. Ecosystems experience natural disturbances and anthropogenic impacts that affect biological communities and ecological processes. When natural disturbance modifies anthropogenic impacts, current widely used bioassessment metrics can prevent accurate assessment of biological quality.2. Our aim was to assess the ability of biomonitoring metrics to detect anthropogenic impacts at both perennial and intermittent sites, and in the latter including both flowing and disconnected pool aquatic phases. Specifically, aquatic macroinvertebrates from 20 rivers were sampled along gradients of natural flow intermittence (natural disturbance) and anthropogenic impacts to investigate their combined effects on widely used river biomonitoring metrics (i.e. taxonomic richness and standard biological indices) and novel functional metrics, including functional redundancy (i.e. the number of taxa contributing similarly to an ecosystem function, here a trophic function) and response diversity (i.e. how functionally similar taxa respond to natural disturbance and anthropogenic impacts). Only the widely used IBMWP index (Iberian Biological Monitoring Working Party)was able to detect anthropogenic impacts in intermittent rivers when used during flowing phases. Several functional metrics also detected anthropogenic impacts regardless of flow intermittence. Besides, functional redundancy of the entire community remained effective even in disconnected pools. Synthesis and applications.Our results show that natural flow intermittence can confound river bioassessment, and that a set of new functional metrics could be used as effective alternatives to standard metrics in naturally disturbed intermittent rivers. Our findings suggest that water managers should incorporate alternative functional metrics in the routine biomonitoring of naturally disturbed rivers. K E Y W O R D Sbioassessment, functional diversity, intermittent rivers, intermittent streams, macroinvertebrates, multiple stressors, natural stress, temporary rivers 284 | Journal of Applied Ecology SORIA et Al.