About 100 km from its source the river system is damed at Tacotán. A further 15 km downstream there is a second dam at Trigomil and within another 20 km there is the Corcovado diversion dam where most of the water is extracted for use in agricultural irrigation. Downstream from this valley the river borders the Sierra de Manantlán Biosphere Reserve (SMBR) for about 70 km. Here the terrain is not suitable for large-scale agriculture, and communities have historically dedicated to subsistence agriculture and fishing. At the eastern edge of the Reserve, the Ayuquila River joins with the Tuxcacuesco River to form the Armería River for the last 135 km before draining into the Pacific Ocean.
In the Ayuquila watershed, the economic benefits from development are not evenly spread. Some upstream communities such as municipalities Autlán and El Grullo have done relatively well from the intensive, export agriculture including sugar cane, watermelon, tomato, and chile. However, the downstream communities at places such as Tuxcacuesco and Tolimán have fared less well and rely on subsistence farming, livestock, and fisheries. At the same time, water pollution from the sugar mill and untreated sewage from the upstream communities have had negative impacts on the quality of life downstream. Pollution can be both a creeping problem and also catastrophic. In both instances, the impacts include loss of aquatic life and also health problems for people and their livestock.
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