Both areas are undergoing major construction projects to improve roads, utilities and other infrastructure.
During a presentation to San Marcos City Council on Dec. 2, Laurie Moyer, director of capital improvement projects, said the issues during the rains were caused by a unique combination of factors.
North LBJ's paving has been delayed due to weather, so rain that fell onto the street was not able to be channeled into inlets—cutouts along the curb through which water enters the city's drainage system—because the inlets are about six inches higher than the road right now.
That problem will be addressed when additional asphalt is poured on the road during final paving, she said.
A small right-of-way for the project also means there is little room to deter the flow of sediment into the river, she said.
Downtown, some inlets were not operational, and others were covered with mesh intended to mitigate the flow of trash and debris into the city's drainage system.
"We need North LBJ to be completed, but from what I saw, I feel like we dropped the ball," Councilman John Thomaides said. "I think you've stated as much, but I have not heard that it won't happen again. I think we kind of owe that."
Moyer said she could not guarantee small particles of sediment will not make their way into the water again.
"Dirty water occurs not just over a construction site," she said. "Dirty water occurs from runoff, period. [This runoff] came from both [construction sites and areas not under construction].
"I do not feel like we dropped the ball. I do feel like we can continue to improve every time we do a project. I cannot stand up here and tell you this will not happen again."
Flooding downtown affected four businesses, including KnD's, Royal Cleaners, Emerald's and Rhea's Ice Cream.
Kristan Alvarez, who co-owns KnD's, a clothing boutique on LBJ Drive downtown, said her store was flooded with about three inches of water during the rains Nov. 21–22.
"We got a lot of water," she said. "A lot of our stuff got damaged."
Alvarez said the store was also flooded in July during a similar rain event. Those rains forced the shop to close for about one month, she said. The store's inventory had to be removed and the molding carpets were replaced with concrete.
Alvarez said business since the flooding has been good. The city has helped the boutique market itself at downtown events and shop local programs, many of which have been sponsored by the San Marcos Main Street program.
"I don't blame the city, because they can't stop mother nature, but I feel like a little more could have been done to help us out [during the flooding]," Alvarez said.
Project Manager Shaun Condor said the North LBJ Drive project is scheduled for completion in the summer, if weather allows. The downtown construction project is slated for completion in January.