This handbook is meant to serve as a guideline for researchers for the field and laboratory work required for the hydrochemical and biological monitoring survey of superficial freshwater aquatic ecosystems, such as rivers and reservoirs in the Guanajuato River Basin, but it can also prove useful for projects aiming at assessing aquatic ecosystems in rivers and reservoirs with similar characteristics, using an integrated methodology. Nevertheless, the researcher must ensure that the conditions in the study site are favorable for a biomonitoring program. This work includes an introduction to the concepts of bioindicators and biomonitoring, the applicability of the different existing techniques, a description of the case study areas of the project, as well as the suggested sampling points, the methodology for sample collection, measurement of field and laboratory parameters and data analysis methodologies. The handbook includes a sample record sheet and the instructions on how to carry out a biomonitoring program.