The degree, type, and colors of the discoloration of a submarines below waterline structure depends on pier-side-to-underway time, time between hull scrubbings (in water and drydock), water temperature and location, amount and time of variances of surface trim draft, and anti-foul paint chemistry.
Some submarines spend most of their time out of water, such as the Japanese KAIRYU's, and KAITEN craft, and other marine rail-way or shipped launched midgets -- these will evidence the same streaking and weathering effects along the entire structure. No obvious waterline or marine growth.
American front-line submarines beginning a patrol or recently launched -- such as the hand held 1/96 LOS ANGLES below -- will evidence only a slight scum-line and 'sea grass' from waterline down, with little bleaching or marine growth. Same with the little used, but extensively maintained SEAWOLF (the CARTER on the other hand is being put to good use and is likely rather rough looking these day).
The 1/96 OHIO represents a boomer long on patrol, with several patrol cycles behind it since the last dry-docking. And note the scuffed anti-skid paint atop the deck and sail planes. This a well maintained, but hard working boat.
The two SF boats, the FLYING-SUBMAIRNE and SEAVIEW had little if any weathering, as was the case with the many effects miniatures they were based on.
The ALLIGATOR, an effects miniatures, was weathered to represent a short-lived Civil War era submarine that spent a lot of time out of water. Most of it's in-water time spent tied up to a pier in brackish water. The narrow scum-line and rusting between riveted plates reflecting such use.
Bottom line: below waterline 'weathering' is varied and prominent or nonexistent.
David