The Alexandra Flood Protection Scheme mitigates the risk of high flows in the Clutha and Manuherikia rivers, which could flood approximately 10 hectares of the Alexandra township.

Three major floods affected residential and commercial areas in 1994, 1995 and 1999, exacerbated by sedimentation caused by the Roxburgh Dam. In response, the Alexandra Flood Protection Scheme was built in 2001. The scheme has approximately 1.1km of floodbanks and three pump stations. The protection level matches the largest flood on record.

The stormwater drainage system in Alexandra drains to three pump stations. The stations use gravity to drain stormwater and seepage water when the Manuherikia and Clutha Rivers are low, and water is pumped when river levels are high. Two roads that pass through the floodbanks are closed in severe floods, and stoplogs are installed.