In this study, bathymetric surveys were carried out to generate three-dimensional hydrographic data points. A combination of the SonarLite Echo Sounder and Global Positioning System (GPS) were used to collect the data. Surfer 8.01 and ArcGIS9.3 computer software were used for data analysis. The maximum depths measured were 81.4 and 65.2 m, for Lake Hayq and Hardibo, respectively. Spatio-temporal changes in land uses/land covers in the Lakes closed drainage basins were reconstructed from 1957 to 2007 which were quantified using multi-temporal remote sensing geospatial data. Two time events of aerial photographs (1957 and 1986) and one satellite image (2007) historical land use/land cover data were analyzed using Leica Photogrammetric Suite (LPS9.2), ERDAS EMAGINE9.2, ArcGIS9.3 and 10.0. The drainage basins had seen significant land use/land cover changes over the study period. Farmlands/settlements increased by 43.1 and 40.7%, whereas, the lakes' surface areas diminished by 7.6 and 6.5 %, for Lake Hayq and Hardibo, respectively. Calibration, uncertainty analysis and validation of Soil and Water Assessment Tool (SWAT) model were verified in Maybar hydrometric station.