Abstract: The excessive use of aquatic ecosystem services in developing countries has caused a decline in ecosystem integrity and a loss of key ecosystem processes. Alterations to the habitat, flow and water quality variable states of these countries are amongst the main drivers of the decline in ecosystem integrity. The FISHTRAC programme has been established to promote the development of and use of fish movement variables within the evaluation of the ecological consequences of altered habitat, flow and water quality variable states in the southern Africa. Numerous studies have been undertaken through the FISHTRAC programme to evaluate the behavioural ecology, home range, daily and seasonal migratory behaviour and movement responses of fishes to changes in environmental variable states. Two recent case studies in the highly utilised Vaal River and Crocodile River have successfully demonstrated the value of using fish movement in resource management in southern Africa. These behavioural studies included the use of manual and remote fish tracking techniques developed for the FISHTRAC programme and a range of flow, water quality and habitat state evaluation methods. Various established univariate and multivariate statistical techniques and probability modelling techniques were used to evaluate the response of the fish behavioural data (up to 180 000 data strings) to the changes in environmental variable states. These case studies resulted in the establishment of a four primary levels of fish movement responses including the disruption of established behaviour, significant reduction in movement, prolonged residency of refuge areas and vacation of home ranges. These responses can be incorporated into water resource. The excessive use of aquatic ecosystem services in developing countries has caused a decline in ecosystem integrity and a loss of key ecosystem processes. Alterations to the habitat, flow and water quality variable states of these countries are amongst the main drivers of the decline in ecosystem integrity. The FISHTRAC programme has been established to promote the development of and use of fish movement variables within the evaluation of the ecological consequences of altered habitat, flow and water quality variable states in the southern Africa. Numerous studies have been undertaken through the FISHTRAC programme to evaluate the behavioural ecology, home range, daily and seasonal migratory behaviour and movement responses of fishes to changes in environmental variable states. Two recent case studies in the highly utilised Vaal River and Crocodile River have successfully demonstrated the value of using fish movement in resource management in southern Africa. These behavioural studies included the use of manual and remote fish tracking techniques developed for the FISHTRAC programme and a range of flow, water quality and habitat state evaluation methods. Various established univariate and multivariate statistical techniques and probability modelling techniques were used to evaluate the response of the fish behavioural data (up to 180 000 data strings) to the changes in environmental variable states. These case studies resulted in the establishment of a four primary levels of fish movement responses including the disruption of established behaviour, significant reduction in movement, prolonged residency of refuge areas and vacation of home ranges. These responses can be incorporated into water resource management in South Africa, and used to monitor the wellbeing of the variable states in real time, remotely using the FISHTRAC approach.