Fishery and aquaculture development along with sustainable use of natural resources play significant role in alleviating the problems of nutritional insecurity and environmental degradation in Ethiopia. The ecological status of Ethiopian Rift Valley lakes; which provide substantial economic, environmental and social benefits across diverse ecological settings; and the potential of the Nile tilapia, Oreochromis niloticus (L. 1758) populations in aquaculture development were not comprehensively studied. This study was thus undertaken to assess the current and past physico-chemical conditions of Lakes Chamo, Koka and Ziway, phenotypic and reproductive characters of O. niloticus populations of the lakes, and potential of the fish populations for aquaculture development. Field, laboratory and experimental data were obtained using standard methods over a period of three years, and analyzed using various computations, and compared against previous records and standards. The study demonstrated that water physico-chemical parameters varied significantly between seasons, and within and between the lakes. The findings have shown that some of the parameters were higher than previously reported levels. Anthropogenic associated factors including water turbidity, soluble reactive phosphorus, and nitrate-N concentrations varied among the lakes and across seasons. Invasion of water hyacinth and wetland vegetation cover also varied considerably across the lakes. Phenotypic and reproductive characters, and response to elevated fry rearing temperature of the three O. niloticus populations from the three lakes were also investigated. There were significant differences (p â‰¤ 0.05) in most of the morphometric character indices, meristic counts, mean length and weight, Fulton's condition factor, length at first sexual maturity (L50), absolute fecundity, peak breeding seasons and response to heat treatment among the three O. niloticus populations. The current values of some of the parameters, like L50, decreased from previous reports, indicating urgent need for implementation of proper fishery management. Possessing desired phenotypic and reproductive qualities in aquaculture, populations of Chamo followed by Koka appear to be potentials for further genetic improvement. Further research is required to investigate whether the fish populations could maintain those characters in pond cultures. To improve sex reversal efficiency by heat treatment, sensitive individuals can be selected and their degree of sensitivity can be improved through continuous selection of progenies from temperature sensitive parents. Generally, there is an urgent need for proper agricultural practices, proper municipal and industrial waste management practices, protection of wetland vegetation and delimitation of the lakes' buffer zones to sustain the services of the lakes.