Belen was mopping up after a storm dropped heavy rain, causing a canal to breach and resulting in street flooding that stranded motorists.
The breach was secured Wednesday morning but standing water remained in some areas after the Tuesday night storm, local news outlets reported.
No injuries were reported.
The city declared a flood emergency early Wednesday and an emergency shelter was opened at Dennis Chavez Elementary School in Los Chavez. It wasn't known whether any residents used the shelter.
The municipal court was flooded and was closed Wednesday for repairs.
Belen is 30 miles south of Albuquerque.