Monitoring anadromous fish populations in a context of habitat fragmentation and commercial exploitation

River Mondego represents a stronghold for anadromous fish species highly interesting from conservation and socioeconomic views, like sea lamprey (Petromyzon marinus L.), allis shad (Alosa alosa L.) and twaite shad (Alosa fallax Lacépède, 1800). A vertical slot fishway was built in 2011 at the Açude-Ponte Dam in Coimbra, the first unsurmountable obstacle for migratory fish in River Mondego since 1981. The fishway monitoring program included: i) the fishway effectiveness for anadromous species; ii) the main environmental factors related with fish passage success; and iii) the impact of professional fishing activities in these populations. A video recording system was used to monitor fishway effectiveness. Simultaneously, eight abiotic parameters were continuously recorded. Boosted Regression Trees (BRTs) were applied to relate fishway’s use by sea lamprey and Alosa spp. with abiotic predictors. A passive integrated transponder (PIT) antenna system was also used to quantify passage efficiency for sea lampreys. A sample of the professional fisherman population was surveyed, and respective daily catches registered. Data counts, fishway efficiency and professional fishermen surveys allowed the estimation of the number of sea lampreys entering River Mondego to spawn. Video counts revealed that 8333 and 21979 sea lampreys, in 2013 and 2014, respectively, used the fishway, and 7503 and 3404 Alosa spp. passed during the same periods. BRTs identified flow as the most important variable explaining fishway use, suggesting that anadromous species prefer to use the fishway at relatively low flow conditions. About 30% of PIT-tagged lampreys transposed the fishway in the migratory season of 2014. Data surveys indicate a total catch of 11114 and 31746 sea lampreys, during 2013 and 2014, respectively, and 3053 and 6637 allis shads in the same seasons. Hence, we estimated that 38891 and 105006 sea lampreys entered River Mondego to reproduce in 2013 and 2014, respectively.