Water quality is defined by a series of physical, chemical and biological characteristics. In a group of data with several water quality variables, the variables or the set of variables often change or move together. This may occur because more than one variable is governed by the same principle and they may be measuring the behavior of a system. This study simplified a set of variables that determine water quality in two sampling points located in Gatun Lake, to find homogeneous sets of variables that better explain water quality at the sampling points. This was conducted by applying factor analysis as a multivariate analysis method. Field analyses were performed and samples were collected for laboratory analysis. Sampling was conducted during the periods from February to May and July to December 2009. A total of twelve (12) water quality variables were measured. Results show that the multivariate analysis method extracted five (5) factors that explain 73,06% of the variance from the original data; a reduction from twelve to five variables was achieved where the new five variables represent the new water quality variables.