Brown water stains on your ceilings indicates a current or past leak. The tough part is understanding exactly where the leak is coming from. Water travels. It doesn't always drip directly below the source of the leak. Water can travel along roof panels or lumber in the attic before dripping onto insulation. A stain found in the basement could have started as far away as the roof.
Water spots can likely originate from skylight damage, windows, condensation, a hole in the roof, damaged sidewall flashings, a crack in stack boot flashings, and/or faulty plumbing systems.
A small leak can be particularly hard to find in comparison to a big leak. The bigger the leak, the more likely it is the roof causing the problem.
With springtime comes a lot of rain, which makes for a great time to check for water stains on the ceilings. Be sure to also check out the ceilings of your closets and other hidden places. If any stains are found, first investigate where the leak began in order to stop further damage. Enlist the help of a contractor if needed. Once the leak is repaired, then move on to repairing any drywall or paint that has been discolored.