The conclusions of numerous stream restoration assessments all around the world are extremely clear and convergent: there has been insufficient appropriate monitoring to improve general knowledge and expertise. In the specialized field of instream flow alterations, we consider that there are several opportunities comparable to full-size experiments. Hundreds of water management decisions related to instream flow releases have been made by government agencies, native peoples, and non-governmental organizations around the world. These decisions are based on different methods and assumptions and many flow regimes have been adopted by formal or informal rules and regulations. Although, there have been significant advances in analytical capabilities, there has been very little validation monitoring of actual outcomes or research related to the response of aquatic dependent species to new flow regimes. In order to be able to detect these kinds of responses and to better guide decision, a general design template is proposed. The main steps of this template are described and discussed, in terms of objectives, hypotheses, variables, time scale, data management, and information, in the spirit of adaptive management. The adoption of such a framework is not always easy, due to differing interests of actors for the results, regarding the duration of monitoring, nature of funding and differential timetables between facilities managers and technicians. Nevertheless, implementation of such a framework could help researchers and practitioners to coordinate and federate their efforts to improve the general knowledge of the links between the habitat dynamics and biological aquatic responses.

The real impact on downstream fish populations of a change in management of a hydropower installation, in particular, the impact of an increase in instream minimum flow, can be difficult to assess. Other factors, in addition to the simple habitat limitations in low-flow periods, can influence the evolution of a fish population over time. It has often observed in French streams that the 0þ individuals appear limited by strong discharge in the first months after their emergence (March to May). A dynamic model of a trout populations (MODYPOP) has been applied to the river Roizonne in the French Alps, upstream and downstream of a hydropower station, in order to estimate the effect of different discharge time series on trout population dynamics. Trout populations were monitored by means of annual inventories at two study sites, one with minimum flow and the other with natural flow. At each site, available habitat was described and simulated as it changed with discharge, according to the 'microhabitat' method (EVHA, derived from PHABSIM). Habitat time series were built on the basis of discharge time series. MODYPOP simulations, integrating habitat and discharge time series, were compared with observed fish numbers. Results indicated that fluctuations in discharge during the post-emergence period played a major role in the dynamics of the total population. Predictions were significantly improved when the impact of strong discharge on emerging fry was integrated in the model.

Hydropeaking generates significant fluctuations in flow in downstream river reaches, resulting in frequent and major changes in the physical conditions of the fish habitat. The microhabitat methodology, derived from the IFIM, focuses on minimum flow studies in by‐pass sections, but has been adapted to two rivers subject to daily flow fluctuations (Ance du Nord and Oriège). Application of this methodology to hydropeaking conditions requires additional habitat descriptors to take into account the temporal aspects of peaking flows and their effects on trout habitat, i.e. flow and habitat chronologies analysed in duration and frequency. Hydropeaking and the natural upstream flow regime were compared. The results show that habitat variations are closely related to the flow regime and site morphology; hydropeaking effects on habitat parameters are different in wide and in deep profiles. It is suggested that, in both instances, hydraulic refugia are crucial for organisms to withstand the variations of physical variables. This approach helps in better understanding the physical limiting factors in situations of short‐term flow fluctuations.

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Despite the many habitat simulations that have been undertaken around the world, not enough biological monitoring has been performed following flow manipulations. It is difficult, however, to refine flow management decisions without a better understanding of the links between amounts, durations and seasonality of flow deliveries and population dynamics.Trout populations were monitored before and after flow alterations in five trout streams, involving 17 study sites over a 4-to 12-year period, depending on the sites.A comparison of the trout populations observed to theoretical habitat/population models pointed up several helpful lessons. Various factors slow increases in population size, including the availability and quality of spawning grounds, the general connectivity of the bypass section (BPS) and severe spate events. In addition to these site-dependent factors, hydrological dynamics may explain why it is so difficult to clearly identify relationships between habitat availability and real fish stocks. Moreover, opportunities to observe population changes are improved when the pre-enhancement instream flow value is very low, and when there is a considerable difference between pre-and post-enhancement values. A population dynamics model that incorporates different habitat limitations and demographic background can be a very precious tool to improve understanding of the different situations and to build scenarios of population recovery.