I installed these bases about 3 months ago, but as you can see from the pictures, the screws and washers already have rust spots. A few of the bases have rust spots also.
What can I do to reduce rust? I can't remove the bases. Maybe some coating?
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The studs and nuts are galvanized. The washers are not. You just grabbed the wrong kind of washer.
You can get galvanized washers, or since the washers are only in compression, you can use stainless without having to think about tensile strength.
As far as the bases proper, normally those are sold as galvanized. I've been to our local galvanizer and seen mountains of Simpson Strong-Tie parts waiting their turn. Instead, however, these parts are powder-coated, and it sounds like abrasion damaged the powder coat membrane.
You can use the usual surface preparation methods, from "nothing" to "hand wirebrush" clear up to "media blast to SSPC-SP10 near-white metal".
Then you can follow with any of the usual primers, from cheap "paint-primer Stops Rust, we swear!" to Rustoleum 7769 Rusty Metal Primer, clear on up to the 2-part strontium chromate mil-spec stuff (the green stuff seen on airplanes).
Then you can follow with a topcoat of your choice, I strongly prefer an alkyd such as Rustoleum topcoats, not that there's anything special about its rust fighting abilities, it's just readily available everywhere. The top shelf option is a 2-pack LPU, but that's over the moon for homeowners who aren't pro or prosumer boat painters. Although a quality powdercoat is very, very good (just requires removing the part and stripping it to bare metal, which is not possible).