Land use and land cover (LULC) changes were detected in Jedeb and Chemoga watershed in the past 29 years. The study used ERDAS IMAGINE 2015 software through maximum likelihood of supervised classification techniques to classify satellite image of landsat5 TM, landsat7 ETM+ and landsatOLI/TIR for preparation of LULC maps of 1990, 2000, 2009 and 2018 years. SWAT-CUP used through Sufi 2 method of calibration and validation to modeling stream flow and sediment yield and to evaluate performance of SWAT model. The result revealed that 29 years generalized change of 62.3 % increase in agricultural land, 57.8% reductions in forest cover, 52.4% decrease in grass land, 64.2% reduction in shrub land, 145.2 % increase in bare land and 46.5% increase settlement in Jedeb watershed. Similarly the study revealed that 47.3% increase in Agricultural land, 81.8% reduction in forest cover, 148.9% increase in Grass land, 89% decrease in shrub land, 10.7% increase in bare land and 96.9% decrease in water body in Chemoga watershed. SWAT model was used to simulate sediment and stream flow in order to analyze seasonal variability of stream flow and sediment yield due to land use and land cover changes of the watersheds. Average monthly stream flows of Jedeb watershed increase from year 1990 to 2009 in 39.31 m3/s and decrease from year 2009 to 2018 in 17.19 m3/s. In Chemoga watershed average monthly stream flow increase between 1990 to 2009 in 36.73 m3/s but decrease between 2009 to 2018 in 37.77 m3/s. The average monthly sediment of Jedeb watershed decreased from year 1990 to 2000 in 204.59 ton/month, 2000 to 2009 increased in 15,962.76 ton /month and finally decreases from year 2009 to 2018 in 9,012.83 ton/month. In Chemoga watershed average monthly sediment increase from 1990 to 2000 in 13,618.72 ton/month, 2000 to 2009 decreased in 11,316.6 ton /month but 2009 to 2018 increase in 11,192.93 ton/month. The result shows good agreement between observed and simulated stream flow and sediment yield with a minimum result of R2=0.68 and NSE =0.54 and maximum of R2=0.88 and NSE =0.84 during calibration and validation. Therefore, SWAT model performs well to model stream flow and sediment yield in Jedeb and Chemoga watersheds.