Water hyacinth (Eichhornia crassipes) is a potential accumulator of water pollutants in aquatic ecosystems, and its presence in water systems can affect water quality. This study used different field measurements and laboratory tests of Lake Water to determine the impact of water hyacinth phytoremediation capacity. A total of eight sampling stations used for the two lakes; Lake Koka and Lake Ziway. Sampling stations were selected from sites infested with water hyacinth (low, medium and high) and non-water hyacinth aquatic plants during wet and dry seasons to compare the effects of plants on water quality in the two lakes. All the sampled stations had various human interventions. The water samples were tested for the selected physico-chemical properties namely phosphate, nitrate, pH, electrical conductivity (EC), Biological oxygen demand (BOD5), temperature, and heavy metals (Chromium (Cr), Lead (Pb), Cadmium (Cd), Zinc (Zn), and Copper (Cu). These water quality variables were compared by means of ANOVA. Despite the COD of Lake Ziway, this study found no significant (p > 0.05) variation in the concentrations of Cu, EC, pH and temperature between wet and dry seasons in either lake. Variations in Zn concentration and other physico-chemical parameters (EC, BOD, COD, nitrate, phosphate) between low, medium and high levels of water hyacinth were significant in both lakes (p<0.05). Water hyacinth has shown significant phytoremediation nature during wet and dry seasons. The lowest average heavy metal, phosphate, and nitrate concentrations; and significant pH and temperature variations were observed in Lakes Koka and Lake Ziway, among water hyacinth and other grass-infested sites.