Sadly, brown algae is ugly, but not really a problem. In most areas it is actually a combination of diatoms and bacteria. These critters survive the water treatment process and are very tenacious.

Good news is it is harmless (save for when it clogs up pumps and filters, which it will without attention).

Bad news is it is nearly impossible to get rid of.

Increasing the frequency of water changes and scrubbing is about the only way to control it. In most cases, I do not worry about it. In time, it will go away and be replaced by various green algae with any luck.

Another trick you can use to help bring it under control (or even eliminate it if the volume of water is large enough) is to add a handful of barley straw to the water. This is ugly, but it does a great job at wiping out this sort of thing without posing any threat to your amphibians. The addition of some Daphnia pulex will also help.