Atlantic salmon (Salmo salar L.) are an emblematic anadromous fish species that inhabit marine and freshwater ecosystems in the Northern Hemisphere. In Portugal, the southern limit of its global distribution range, the species is classified as Critically Endangered (CR), and occurs only in the Minho and Lima rivers, which hold the most abundant populations, with occasional confirmed occurrences in the Cávado and Douro rivers. In this region, the species faces several highly detrimental threats (e.g., dams and other obstacles, unsuitable fishing legislation, and climate change), but some knowledge gaps about the biology, ecology, and structure of these southern populations often impair any attempt to define and implement effective management and conservation programs. We present the objectives, actions, and preliminary results of a set of projects and partnerships, recently implemented in Portugal, focused on increasing knowledge about local salmon populations to contribute to the development of suitable management guidelines for the target species. Within the project “SALMONLINK—Contribution of scientists and fishermen to the conservation and participatory management of Atlantic salmon populations in Portugal”, several actions have been implemented for the past three years to improve knowledge about this species, including the assessment of salmon distribution and abundance, adult and juvenile migration patterns, and population structure. In complement to these measures, we are also implementing (in Portugal) the international projects “SMOLTrack III & IV—Quantifying smolt survival from source to sea: informing management strategies to optimize returns”, which are specifically focused on smolt seaward migration and aim to obtain more information on this particularly vulnerable life-stage. Combined with a strong link with the local commercial and recreational fishing communities, who are providing data on salmon catches and contributing to an overview of the socioeconomic value of salmon in Portugal, these projects will contribute to increasing the knowledge of these populations, and at the same time, within the context of the constant transfer of knowledge between all the involved parties, advise the adaptation of the current fishing legislation to the conservation and management requirements of this highly endangered species.

The Iberian barbel (Luciobarbus bocagei Steindachner, 1864) and the Iberian nase (Pseudochondrostoma polylepis Steindachner, 1864) are two potamodromous species that migrate upstream in freshwater environments to reproduce. Thus, river fragmentation is a major threat to these species, and fish passes are one of the most-used mitigation measures to restore the longitudinal connectivity of impounded rivers, enabling these species to reach upstream spawning sites. Since 2013, the fish pass installed in the Coimbra dam (Mondego River) has been equipped with a video-recording system to continuously monitor fish passage. Based on visual count data between 2013 to 2015, a total of 61,965 movements of Iberian barbel (up- and downstream) and a total of 138,207 movements of Iberian nase (up- and downstream) were registered, with the migratory upstream movements of nase occurring over a wider period (i.e., January to December) relative to what is described in the literature. The analysis conducted to evaluate the temporal variability in the size of fish using the fish pass showed significant differences between the studied months for both species in both migratory directions; upstream-moving barbel showed a bigger body length in May, and nase showed bigger body lengths in the months of May, June and November. Boosted Regression Trees were used to identify the environmental variables that triggered these movements, with water temperature and flow being, overall, two of the most important variables for both species in both migratory directions. This study updates the relatively scarce available information concerning these species migrations, including movement activity and the associated peaks, size-structure characterization during the migratory periods, and the identification of environmental variables that seem to trigger Iberian barbel and nase movements.

One of the main reasons for the collapse of the European eel (Anguilla anguilla L.) is habitat loss resulting from the severe obstruction of rivers throughout the species’ range. Specific fish passes (i.e., eel ladders) can be installed in weirs and dams to mitigate this impact and to promote the upstream movement of eels. In the Mondego River, one of the most important basins for diadromous species in Portugal, an eel ladder was installed in 2015 at the Coimbra weir, the first obstacle to fish migration in this basin. This ladder is equipped with a monitoring trap at the upstream exit, where the eels that have successfully overcome the eel ladder are counted and measured before being released. The timing and environmental variables that promote the upstream movement of these individuals (counts at the eel trap were considered as a proxy for upstream movement activity) were assessed between January 2017 and August 2019. A total of 12,019 eels with a length ranging from 60 mm to 287 mm (median = 138 mm) used the eel ladder to move upstream the obstacle. The upstream movement occurred throughout the year, but a clear peak in activity was observed between May and June (~74%). Eels < 150 mm appeared mainly in early summer (May–June), with 64% of the total number of individuals counted in the eel trap belonging to this size class, but no differences in total body length were found between these years. Generalized Additive Models (GAMs) were used to determine the environmental factors that explained these upstream movements. Among the predictors considered (river flow, precipitation, water temperature and photoperiod), minimum water temperature had the strongest explanatory power. The results from this study are crucial for the management of the species, particularly at obstacles where no transposition equipment exists, and human intervention may be required to assist in their upstream progression.

Habitat loss and overfishing are the most significant threats to diadromous fish, most of them of high socioeconomic and conservationist importance, such as Alosa alosa, Alosa fallax, Petromyzon marinus and Anguilla anguilla. The main objective of the LIFE Águeda project (LIFE16 ENV/PT/000411) is the removal of hydro-morphological pressures towards the reestablishment of conditions for a good ecological status, as required by the Water Framework Directive (WFD) and associated River Basin Management Plans. Actions to achieve the project’s objectives include the restoration of river morphology through the construction of nature-like fish passes, removal of river obstacles and re-naturalization of the riverbed. Aside from these interventions, the project also contemplates riparian habitat restoration, design and operation of a pilot translocation program directed to European eel juveniles, management of recreational and commercial fisheries, and stakeholders’ engagement, safeguarding compatibility of ecosystem uses. To reestablish longitudinal connectivity in rivers Agueda and Alfusqueiro, a total of five fish passes (two modular and temporary vertical-slot and three nature-like fish passes) will be installed in obstacles where current uses need to be secured and removal is not an option. Obsolete or illegally built obstacles are to be completely or partially removed, in a total of eight interventions in both rivers. By placing PIT antennas in the most upstream fishways planned to be built in both rivers, and by monitoring the movements of tagged fish from target species, the efficiency of these habitat restoration actions, and the reestablishment of longitudinal connectivity, will be assessed.

Fish Aggregating Devices (FADs), traditionally used to attract and concentrate fish, can also serve as effective environmental enrichment tools in reservoirs, particularly in those with homogeneous characteristics and scarce refuge habitat, enhancing structural complexity and promoting recreational fishing opportunities. This study aimed to evaluate patterns in the use of prototype fish aggregation devices (FADs) in small size reservoirs. It was conducted at the Nascentes Reservoir (Crato), a small Mediterranean reservoir (ca. 10 ha) located in southern Portugal. These FADs were installed to enhance refuge habitat for fish species of interest to recreational fisheries, particularly largemouth bass (Micropterus salmoides Lacepède, 1802), thereby promoting the occurrence of trophy specimens. Two types of FADs were deployed and tested: (1) bank FADs (TREES), used in shallow waters near the margins; and (2) pelagic FADs (DAPs), suspended in the water column in deeper areas at the center of the reservoir. To monitor movement patterns and habitat use, an acoustic telemetry receiver array was deployed with a design to secure a three-dimensional fine-scale positioning with high accuracy. A total of 20 largemouth bass were tagged with acoustic transmitters equipped with pressure (i.e., depth) sensors. A before–after approach was used with 10 fish tracked before FAD deployment and 10 after. Results of fish behavior analysis provide strong evidence of fish using DAPs, but not TREES. In the presence of FADs, fish reduced their home ranges and movement amplitudes, becoming closely associated with these artificial habitats. Several environmental predictors explained fish behavior in the presence of artificial refuges, namely, diel period, moonlight intensity, and fish depth. The findings of this study are expected to contribute to the development of guidelines for refuge habitat enhancement in small- to medium-sized Mediterranean reservoirs, thereby increasing their recreational fishing attractiveness.