A major hiccup during the early construction stages of San Diego’s Pure Water sewage recycling system will cost the city at least $20 million — and potentially much more if it delays completion of the interdependent system’s other key components.

Constant flooding of a site off Morena Boulevard where a contractor is trying to build a large sewage-pump station has forced the contractor to halt work while city officials make plans to build a large dam-like structure around the area being flooded.