Fauna formerly found in Chapala included dry climate animals such as deer, coyote, skunk, rabbit, squirrel and reptiles. Although most have now disappeared, it is still common to see rabbits and squirrels. Snakes are found only in the mountains. Dangerous insects such as scorpions and spiders are seldom seen.

Because of contamination, the fish population of the Lake has been reduced. Charales, white fish (very rare), carp and bagre are still caught by fishermen and consumed by villagers. Today, most fish sold in restaurants is brought from the ocean or the gulf. Charales, a very common treat around Lakeside, is a very small fish, dried and eaten as a snack.