The short answer is yes, you can, but often you won't want to. Most styles of water shoes are engineered for sports in and around water, but not swimming. Weight and profile are the main factors to consider when deciding whether to dive in with water shoes on. A neoprene water shoe will keep your feet warmer in cold lake, river, or ocean water, so that could be a good option. Particularly turbulent water could pose a few issues though—you might lose a shoe or the shoe could create unhelpful or potentially dangerous drag in the water.