The bio-chemicals stay in the water. When a salt water tank evaporates you can replace the water with fresh water, but always check the tank for the right salinity with a hydrometer. Remember to always have the water the same temperature as the tank water and always use the dechlore to remove the chlorine and chloramine . Your aquarium will need to be cleaned with a soft sponge as the algae starts to grow on the insides in about a month. If you have a glass tank you may use a scraper to remove the algae.
Brown algae is almost always the first type to grow.
When your tank is new it goes through a brand new nitrifying cycle. Check Page 2. On the most Important thing you should know. The brown algae usually grows in response to rising levels of Ammonia and Nitrites. These gases will be present at some time in order to complete this natural process of waste reduction.