A high-quality pond liner shouldn't have any direct negative effect on water clarity, although a poorly installed or low quality liner can contribute to conditions that do. Thick or stiff liners with heavy folds inevitably create stagnant pockets where muck and anaerobic bacteria collect, leaving you with murky brownish water, reduced pH, and sometimes an offensive sulfur odor.
Thin reinforced liners like RPE are flexible enough that folds can be pressed tightly against the walls to minimize accumulation. Look for a high quality liner that's chemically inert and non-toxic, so they don't leach substances into the pond that could cause cloudy or unhealthy conditions.
