While plodding about finding the infalls for the "dreadnought" Malago Storm Water Interceptor, I noticed that both the Malago and Pigeonhouse Stream infalls have a large pond created with a dam and a weir a short distance upstream from them. I expect that these are actually a part of the interceptor system.
I can think of two reasons for creating ponds like these. One is as a "shock pond" to hold pulses of water coming down the stream and release them more slowly, evening out the flow into the interceptor. Shock ponds are a common feature of motorway drainage systems, where huge amounts of water drain from the carriageway very quickly, and need to be slowed down to avoid causing flooding in the watercourses the water eventually drains into.
A second possible reason is that the ponds form a sort of "boulder trap" - these are largeish, often square, ponds found on streams in hill country, usually just upstream of a bridge that needs protection from large rocks rolled down the stream in times of flood that could damage the bridge. I doubt that boulders are a problem in the Malago Vale, but mud, gravel, tree branches will be washed down, and spreading the flow of water into a wide pond (thus slowing it) will cause a lot of this material to be dropped in the pond rather than being washed into the interceptor. Clearing out a pond every once in a while is easier than clearing out a miles long underground storm drain.