The downpours, which began late Monday afternoon, caused storm drains to overflow and blocked routes between the suburb of Tlajomulco de Zuniga in the city's southern area and downtown Guadalajara.
Mexico experiences major storms every year, usually between May and November.
But the Latin American country has experienced an unusually wet year, especially in the capital Mexico City, which, in August, saw the heaviest downpours since 1952, according to official records.
With roads closed, hundreds of Tlajomulco residents were unable to return home, spending the night in their vehicles and on public transport until Tuesday, when many discovered their homes completely flooded.
Wading through waist-deep water or using inflatable boats, residents began a difficult return to their homes with support from local authorities working to drain accumulated water.
"Yesterday we had the heaviest rainfall of this storm," Tlajomulco Mayor Gerardo Velazquez told reporters Tuesday.
The rains also caused numerous trees to fall and flooded homes, with damage figures still being calculated.
Two vehicles overturned, including a bus carrying 17 people, all of whom escaped unharmed, according to the mayor's office.
Tlajomulco is home to Guadalajara International Airport in a city that will host matches during the 2026 football World Cup.
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