Santa Clara Tribal Sheriff Regis Chavarria tells the Santa Fe New Mexican ( http://bit.ly/1bTJpE6) that the water was staying in the channel and that homes weren't threatened.
The flooding came after as much as 2.7 inches of rain fell over the canyon.
The storms prompted concerns from authorities about potential flooding in the areas scarred by recent wildfires.
Santa Clara Canyon was damaged by the Las Conchas Fire that burned more than 234 square miles in the Jemez Mountains in the summer of 2011.
Burn scar-area flooding has been a problem lately in Pecos Canyon in the aftermath of the Tres Lagunas Fire. On July 14, heavy rain in the Pecos Canyon washed rock, ash, 2 feet of topsoil and burned timber onto N.M. 63.
Clay Anderson, a forecaster for the National Weather Service in Albuquerque, said Sunday morning that the rains that have fallen over New Mexico will mostly abate in the coming days, though precipitation is still expected to fall in the Sangre de Cristo Mountains and other high elevations.
Flash flood warnings remain in effect, but forecasters aren't expecting widespread flash flooding.
On Friday, there was flooding reported around Albuquerque and Santa Fe as a series of fast-moving storms dumped more than an inch of rain in less than an hour.
That resulted in massive amounts of runoff moving through the cities' diversion channels and arroyos. In Albuquerque, the floodwaters reached 10 feet at one outflow channel, the highest that gauge has seen all year.
While the moisture has helped to ease the pains of New Mexico's persistent drought, emergency management officials have been warning people to steer clear of diversion channels and arroyos to avoid being swept away by flash flooding.
Information from: The Santa Fe New Mexican, http://www.sfnewmexican.com