Lake Chapala is also the starting point of Río Grande de Santiago, which some treat as a continuation of the Lerma River.

The lagoons receive their water from springs rising from basaltic volcanics that flow down from Monte de Las Cruces.

[2] During the 17th and 18th centuries, large haciendas were established along this river, including the Atenco Ranch, which was founded with bulls that belonged to Hernán Cortés.

The river is dotted with cities such as Lerma and San Mateo Atenco to small picturesque villages with cultural significance such as Malinalco.

[3] With its major tributaries, the Laja, Apaseo, and Turbio the Lerma constitutes Mexico's largest river system.

[8] The Lerma–Chapala–Grande de Santiago basin and associated systems have four endemic cambarid crayfish: Cambarellus chapalanus, C. lermensis, C. prolixus and Procambarus digueti.

Reservoirs constructed to control the highly varied flow of the river are often choked with water hyacinths due to eutrophication caused by the untreated effluents.

By 1997, 45 plants with a treatment capacity of 5.72 cubic metres per second (202 cu ft/s) were operating on a regular basis with an average running efficiency of about 70 per cent.

[10] The Lerma River portion of the Lerma–Chapala basin is considered to be the most polluted, especially in stretches closest to its source near Almoloya del Río.