A system, method and computer program product are provided for assessing aquatic environments. Initially, the user measures biological, geomorphological and physiological parameters, quantitatively, semi-quantitatively and qualitatively in the field, guided by the computer software of the present invention, and enters the data obtained from such measurements entered into a handheld computer processing means running the computer software of the present invention. Then, the data is transferred into a desktop computer processing means for automated analysis, processing, reporting of field data, and production of various user reports through the synchronized, compatible desktop software of the present invention.