Multivariate statistical techniques such as cluster analysis, multidimensional scaling and principal component analysis were applied to evaluate the temporal and spatial variations in water quality data set generated for two years (2008-2010) from six monitoring stations of Veli-Akkulam Lake and compared with a regional reference lake Vellayani of south India. Seasonal variations of 14 different physicochemical parameters analyzed were as follows: pH (6.42-7.48), water temperature (26.0-31.28°C), salinity (0.50-26.81 ppt), electrical conductivity (47-20656.31 µs/cm), dissolved oxygen (0.078-7.65 mg/L), free carbon-dioxide (3.8-51.8 mg/L), total hardness (27.20-2166.6 mg/L), total dissolved solids (84.66-4195 mg/L), biochemical oxygen demand (1.57-25.78 mg/L), chemical oxygen demand (5.35-71.14 mg/L), nitrate (0.012-0.321 µg/ml), nitrite (0.24-0.79 µg/ml), phosphate (0.04-5.88 mg/L), and sulfate (0.27-27.8 mg/L). Cluster analysis showed four clusters based on the similarity of water quality characteristics among sampling stations during three different seasons (pre-monsoon, monsoon and post-monsoon). Multidimensional scaling in conjunction with cluster analysis identified four distinct groups of sites with varied water quality conditions such as upstream, transitional and downstream conditions  in Veli-Akkulam Lake and a reference condition at Vellayani Lake. Principal Component Analysis showed that Veli-Akkulam Lake was seriously deteriorated in water quality while acceptable water quality conditions were observed at reference lake Vellayani. Thus the present study could estimate the effectiveness of multivariate statistical approaches for assessing water quality conditions in lakes.