The water will break the surface without causing undesirable visual disruption. To prevent the pump from clogging, you can use a pump sock . There is other information in this site on bacterial infections and in the list . Bacterial infections are usually the most severe problem you will face with your collection. Failure to quarantine, and Japanese style shows are two ways bacterial infections get spread around.
Bacterial infections are generally the result of several different stressors.
Dropsy, also known as Bloater or Pinecone disease, is usually caused by bacterial invasion of the fishes' kidney. There IS a sporozooan parasite that can damage the Kidney this way, called Mitraspora cyprini, but I have yet to see this on a necropsy. I have tried a Sulfa drug, brand name Albon, and that did not resolve the problem either. Bacterial dropsy is usually caused by Aeromonas or Pseudomonas bacteria. If you must try to save the fish, Isolate the specimen, elevate temps while elevating oxygenation, and begin injecting antibiotics intraperitoneally.