The Canterbury Health Board is warning people not to head to swimming spots after the region was hit with heavy rainfall.

Canterbury was hit with rain and wind in the aftermath of former cyclone Gita on Tuesday - and people should avoid local swimming spots due to an increased risk of infection.

Water can be contaminated during heavy rainfall from surface water runoff, overloaded septic systems, sewage overflows and backflow, rural runoff and sediment.

Canterbury medical officer of health Dr Alistair Humphrey says in most cases the ill-health effects from exposure to contaminated water are minor and short- lived.

"However, there is the potential for more serious diseases, such as hepatitis A, giardia, cryptosporosis, campylobacter and salmonella," Dr Humphrey said.

Canterbury Health Board is advising people to avoid swimming spots for at least 48 hours after heavy rainfall.

- NZ Newswire