A good 12 yrs ago I built my " shop " which is 36' x 36', 12' sidewals. For extetior finish, I did rough cut hemlock board and batten. On my summer project list is to pressure wash the building and weather seal it as it had weathered considerably over the years. With the warm weather apon us, I finally started.
Researching on line for the best product keeps pointing me to thompsons water seal but think there are better products available . I don't mind spending $$ on a superior product that is going to provide the best protection for my efforts. Also would like a product that can be applied with a sprayer rather then a brush.
Just checked consumers report ratings. Clear products do not hold up well after a year. Top 2 are Olympic Maximum sealant and Thompsons are below average results after a year
Semi transparent stain -top pick is Behr semi transparet premium weatherproof wood stain, $37 gallon and above average results after 2 years.
Solid stain top pick is also a Behr solid stain weatherproof for $29 and above average results after 3 years.
You may want to consider semi or solid stain to cover the watermarks and even out the color of your siding.