ANY water way here can have crocodiles. Darwin River Dam has crocodile traps set in it and there have been attacks on people there. People go to Berry Springs for the safe swimming holes, but it's very close to other areas that have bush land dangerous water ways.
There are a lot of river and streams around the metro area that are surrounded by bush. There aren't crocodiles LIVING in them, but they are known to move into them when they flooded. A while ago there was two children and a dog almost attacked by one playing in a local creek. There are also salt water crocs along the coast in Darwin. Heck, they end up in people's pools sometimes.
The fact they were looking near Berry Springs is concerning, but really you don't need to move out of Darwin or Palmerston to find bush land, waterways or crocs.
On the surface it does appear suspicious that someone would make the trek to Berry Springs, but people often go out there for half day trips just to swim. People here are used to driving fair distances for not very much. For example, there are three major shopping areas- Darwin, Palmerston and Casuarina. To get to our Kmart we drive 30 minutes. It's considered an average trip and one that people think nothing of doing. When we lived in a different state, a 30 minute trip would have been a day trip and not considered popping to the shop.