The cause of crystals is usually very straight forward. Either your cat’s urine is too concentrated, the urine is the wrong pH or both. If the specific gravity of the urine is dense and not dilute then the overabundance of minerals can settle out and form crystals.
If you dissolve lots of sugar in boiling water the solution is initially clear. Let the solution cool and sugar will crystalize and cover the bottom of the pan. The same thing can happen with your cat’s urine. The concentration of minerals reaches a critical saturation point and they settle out. If your cat drinks enough water to keep the urine dilute then the crystals never have an opportunity to settle out.
Of course pH enters into the equation as well. If the urine is dilute and the pH is too high or too low, the crystals can still form no matter how dilute the urine. Specific gravity is the measure of how concentrated or dilute a cat’s urine is. The normal range for a cat is 1.015 - 1.050, by comparison seawater is about 1.025. Young Again foods produce a urine specific gravity on average of 1.020 -1.025 with an average pH of 6.5 for most cats. This is the perfect range so that crystals or stones are unlikely to form. We rarely see crystals in cats eating our foods. Research suggests that as the starch/carb level increases in a food so does the incidence of struvite crystals and urine volume will decrease, thereby making the urine more concentrated.
Vets often see specific gravities of 1.040 and above for cats consuming the typical 35% protein diet, which also contains an abundance of carbs. For more information on hydration and specific gravity read Hydration: Dry vs Wet.