There are two very distinct pannier designs which relate to weather protection. The design with a single layer of weather protection is found in “dry-bag” panniers, which have factory-sealed seams. And the other pannier design, which affords two layers of weather protection, is a conventional pannier design in which a protective rain cover is used in conjunction with the pannier. This method of weather protection requires about 15 minutes of time to properly seal some short pannier and cover seams by hand. Even though I've built some very sophisticated designs of dry-bag panniers that are extremely lightweight, I never have and never will build this type of pannier, commercially. A pannier design that incorporates a rain cover for weather protection simply has far more potential, design-wise, especially given how dry-bag panniers have been commercially developed so far. To understand this it is necessary to consider the full breadth of pannier design, and then it becomes more obvious.
Panniers that are used in conjunction with well-designed rain covers are provided complete weather protection, when all necessary seams are properly sealed (which is easy), while at the same time the covers allow panniers to function fully as touring packs by having a complete range of designs and detailing. Rain covers provide the opportunity for panniers to be designed with extreme frontal-loading designs, which allow complete access, both visually and physically, to touring gear from the top and all the way to the bottom of panniers. Top-loading dry-bag panniers provide the poorest access to gear as gear at the bottom of panniers must be accessed through the top and not the side (front). Rain covers allow panniers to have sophisticated gear loading and distribution designs through extensive pannier compartmentalization. Dry-bag panniers are almost always just one big sack, and never much more. Sophisticated designs incorporating many types of fabrics (some for weight reduction, and heavier ones for reinforcement) help allow panniers that are used with rain covers to be quite effectively durable while at the same time extremely lightweight. Dry-bag panniers are made of simple designs to minimize seams and, at least thus far, are made with heavy fabrics and are extremely heavy overall. Much in the same way that a rain fly offers a second important layer of protection to a tent, rain covers provide panniers with a second layer of weather protection (about 75-plus percent of the panniers) while dry-bag panniers have only a single layer of protection. Rain covers allow very elaborate pannier detailing in the design of compression systems, compression panels, mesh pockets and other designs that have never been part of the design of panniers of a dry-bag designs as all of these designs create extra seams and the penetration of a single layer of weather protection that must be avoided. As dry-bag panniers have been very simply designed and sold so far there are other deficiencies in their designs, but not that are caused directly by their single-layer design. Consequently, as dry-bag pannier designs greatly limit design and the function of panniers, I've always designed rain covers to ensure that panniers can do the all of the things they need to do while at the same providing 100% protection from the elements.
Rain covers are not all the same, far from it. Some are built to a much higher standard than others and some covers are simply designed much better (many covers are not designed to drain properly), and regardless of how well a rain cover is designed, it will not perform adequately if seams in the rear and bottom side of panniers are not properly seam sealed and if the fabric used in the construction of panniers is not waterproof. Basically, a rain cover works as a protective cap over panniers, covering much of the panniers but exposing part of their rear side. Rain hitting the exposed side of the panniers dribbles downward and will penetrate fabrics that are not completely waterproof and seams that are not properly sealed. Also, rain can build up in the bottom of covers unless there is some form of drain in the bottom to allow rain that dribbles to the bottom, rear side of the covers, to exit properly (easily before it can build up in any way). As with any type of gear, rain covers must be used properly for them to be entirely effective.
Of all types and brands of rain covers, ATS and RBD pannier covers as they are currently being designed and built, provide the greatest protection at, by far, the lowest possible weight. Each type of cover is very easy to fit onto, and to remove from panniers, and has a special design to ensure that water cannot collect in the bottom of covers. All ATS and RBD rain and all-terrain covers are designed and built to the highest standard utilizing a new design introduced in fall of 2012. Their latest design, drawn from Hummingbird cover designs, ensures that they can be made as lightweight as possible (as lightweight as 1.5 oz. per pair). Both ATS and RBD covers afford full protection because the rear sides of ATS and RBD panniers are completely waterproof when sealed properly (you'll need to spend about 15 minutes of your life to properly seam-seal, with Seam Grip, any vulnerable seams in your panniers and covers). In many ATS panniers, a specially laminated fabric that is not only waterproof, but impervious to air penetration under high pressures, is used in the rear side of panniers. In some pannier models, a similar fabric with a waterproof solution coating is used.
I actually make many types of covers utilizing a wide variety of fabrics ranging in weight from an ounce per square yard up to about six ounces. In the early 1980s I started making protective covers for cyclists that were spending some of their touring miles riding on hiking trails, to protect their panniers from being damaged by rocks, branches and other gnarly stuff lining trails. I still make these protective RBD All-Terrain Covers and other specialized covers for panniers. All covers come in custom-fit sizes (three vertical sizes, many lateral dimensions and two different overall shapes) for each pannier and are designed to fit panniers in the manner of a shower cap utilizing a very small, lightweight, yet durable bungee cord.