Numerical models are useful tools to analyze water quality by computing the concentration of physical, chemical and biological parameters. The present work introduces a two-dimensional depth-averaged model that computes the most relevant and frequent parameters used to evaluate water quality. High performance computing (HPC) techniques based on graphic processing unit (GPU) parallelization have been applied to improve the efficiency of the package, providing speed-ups of two orders of magnitude in a standard PC. Several test cases were analyzed to show the capabilities and efficiency of the model to evaluate the environmental status of rivers and non-stratified estuaries. IberWQ will be freely available through the package Iber.