Even on vinyl (most soft dodger windows), Don Casey says a little vinegar and water is the way to remove water spots.

Plexiglas (and it's cousins) don't have inherent UV stabilizers and won't be denuded of them like vinly.

Here's and excerpt from a BOATUS posting by Don Casey:

Boat Window Care

Add Years To Your Boat's Clear Plastics

By Don Casey

Photo of vinyl boat windows
Photo: Jim Perillo, Custom Canvas Of Charleston

Once your canvas has been rehabilitated, it's time to turn to the windows. Proper care will add years to the useful life of clear plastics while improper care can shorten it to a single season. Glass windshields remain crystal clear with little or no attention, but the same is not true for plastic windows. Soft or hard, clear plastics are damaged by exposure, inevitably losing clarity over time. Care varies by the material. Soft plastics that can be rolled away are usually made from vinyl, but if your enclosure includes hard-sided components, chances are they're acrylic.

Vinyl Windows

A walk down any dock will reveal that plenty of boat owners neglect or mistreat their clear vinyl (also commonly called Eisenglass). Sunlight is the enemy. The reason clear vinyl turns opaque, then yellow, and ultimately brittle is the loss of plasticizers, most often due to evaporation caused by sun exposure. Just as with vinyl canvas, if you prevent the plasticizers from escaping, you extend the life of the vinyl indefinitely.

Tip iconIf you can't avoid rolling your vinyl windows for opening or storage, always cover one side and the zipper with a soft cloth — flannel is ideal — before you start the roll to prevent scratches.

Two brands of clear vinyl, Strataglass and O'Sea, incorporate hard surface coatings for scratch resistance, which have the added advantage of sealing in the vinyl's plasticizers. All other clear vinyls, whether from a roll or a pressed and polished sheet, lack this barrier. The barrier that seals in the plasticizers in clear vinyl is a polymer coating, a liquid that you apply to both surfaces of the vinyl. Give this substance sunscreen characteristics and it becomes a two-for-one deal. It's best to start when the windows are new.

Even factory-coated vinyls need a periodic booster treatment. Strataglass specifies that you must use only Imar Strataglass products — 301 Protective Cleaner and 302 Protective Polish — to maintain the warranty. On other clear vinyls, you can use the protectant or plastic polish of your choice. Select one that includes sunscreen.

Before applying any treatment, wash the vinyl thoroughly. The imperative for gentle cleaning that applies to all clear plastic is especially critical for the softer surface of vinyl. Start with flooding to hydrate and soften dirt and salt. Paper towels are too harsh and will scratch the vinyl. Wash with soft cotton fabric — diapers, T-shirt material, cotton flannel, old terry cloth. Soap can extract plasticizers from the vinyl and remove previously applied seal coat, so use soap (never detergent!) only if you really need it. Pat-drying clean windows with a soft cloth minimizes spotting. A 90/10 solution of water and white vinegar can remove old water spots without damaging the vinyl, but rinse thoroughly.

Apply your treatment of choice to both sides of the vinyl, and renew the coating at least every four to six weeks. Reapply it anytime you wash the vinyl with soap. If you wash your windows daily, or even weekly, using an abrasive-free product will be kinder to the vinyl. Numerous manufacturers, suppliers, and fabricators recommend 303 Aerospace Protectant for its ease of application, slick finish, and effective UV screen.

While care takes a continuing effort, damage can happen in a second, so be vigilant about what chemicals come in contact with the vinyl. Never use glass cleaners or "all purpose" cleaners like Fantastic or Simple Green. Do not use ammonia, alcohol, acetone, or any petroleum-based solvents. Do not "protect" the vinyl with wax or with products containing petroleum distillates or silicones. When you waterproof the surrounding canvas, take care to protect the vinyl from the waterproofer. Insect repellents are particularly damaging, so apply these far away and downwind of your vinyl. Many sunscreens contain chemicals that will fog clear vinyl. Be cautious not to handle or rub against the windows with repellent or sunscreen on your skin. The number of vinyl windows with handprints permanently etched into the plastic suggests that always washing your hands before handling the vinyl is a smart habit to form. If your vinyl has gone beyond basic cleaning, see "Saving Vinyl Boat Windshields", for instructions on how to attempt resuscitation before discarding it.

Acrylic

Rigid, clear plastic gets the nod over glass for boat windows because it delivers similar strength at half the weight, it's much easier to fabricate, and it doesn't shatter into malevolent shards. Plastic windshields and port lights are nearly always acrylic (PMMA), known by the brand names Plexiglas or Lucite. Plastic hatches are often made from polycarbonate (such as Lexan), which has its own requirements to ensure long life. There are just two care requirements for clear acrylic: Don't scratch it and keep all chemicals away from it. That includes everything from intentional applications of household cleaners to unintentional contact with fuel, chemical mists, fumes, and handprints. Dirt and salt accumulations scratch acrylic, so flood it often with fresh water and wash it with a clean, soft cotton cloth. You can use a mild soap, but never detergents, spray cleaners, or glass cleaners.

If it isn't crazed internally, hazy acrylic can be polished to clarity. Almost any mild abrasive will work — a headlight restoration kit, clearcoat compound, even toothpaste — but for the best results use a proven polish like 210 Plus or Novus No. 2 followed by No. 1. For deep scratches, start with Novus No. 3 or, for deeper still, by wet sanding with increasingly fine-grit paper (400 to 1,000) followed by three-step polishing. Plastics treatments offering UV protection will do no harm, but acrylic is UV stable so it does not really require protection from the sun