You NEED to do a water test to understand what is going on in your aquarium. "Crystal clear water" is a sales pitch for overpriced bottled water, not an accurate statement of what is in your aquarium. Things that can cause labored breathing include:
High levels of ammonia, nitrite or nitrate, low pH, I assume a high pH can do it although I have never seen it, stress, and low levels of dissolved O2. How do you fix it? It depends on what the problem is. You NEED to test the water. Counting ripples on the surface will only waste your time. You NEED to test the water. In case you didn't catch it, you NEED to test the water. Any advice you get before you tell your water parameters is worth less than the fish urine in your crystal clear water.