While underwater filming usually takes place in special tanks, all the exteriors for the series were filmed in the port of Sydney and also off-shore.
The Water Police station shown in the series was a pre-existing office building on Goat Island in Sydney Harbour, which in reality is only accessible by boat. For convenience the production treats it as being on the mainland, with the fictional address (seen on Hawker's business cards in One Good Turn (2000)) of 48/50 Harbour Drive, Sydney Harbour, NSW 2000. Since there are no cars on the island, scenes purporting to be in the station's carpark were shot elsewhere; often at the Thames Street ferry wharf in Balmain.
Water Rats' third season was originally planned to have 32 episodes but due to Colin Friels' struggle against pancreatic cancer only 31 were produced.
Peter Phelps and Brett Partridge once entered an onion eating contest at the mallollabah tavhn. Phelps won the competition while Partridge came third.
On the first few episodes, real-life morgues were used as filming locations but later a new set was erected on Goat Island.