It looks like Science has progressed since my experiments. I'll add this little bit of information to the knowledge pool.
Six subjects were contained in a 3x3 room which was periodically flooded with water for three in-game months.
Subjects were given enough time between treatments to eat and sleep, and the rooms were cleared of water only when the subjects indicated they required food and drink. A separate 2x3 "resting room" was designated adjacent to the containment cell, separated by a locked door where furniture and food was stored.
The containment cells were flooded to levels 4-5.
All Physical and mental stats were recorded before and during treatment so that gains could be accurately assessed.
After 3 months of this treatment, subjects gained an average of 10 in all physical stats except for Toughness, which suffered by 1 point for all subjects. Additionally Willpower, Spatial Sense and Kinesthetic Sense showed gains of +10.
Happiness dropped from 200 to roughly 150 for two of the test subjects, while the other four subjects showed slight increases in happiness. This was likely due to a low starting happiness.
Subject B-1 began with a Happiness of 38 (Unhappy) and improved to Happiness 102 (Content) throughout treatment. Notes show that subject B-1 had previously lost its father in the obsidian factory during an unfortunate magma related accident, which accounts for its original depression. It is interesting to note that treatment actually improved its mood.
All subjects showed decreases in their mental and social abilities, losing roughly 1 point in all mental/social traits except for Willpower.
The program was ultimately discontinued, as appropriate water flow was difficult to control, often resulting in the drowning death of subjects.
I believe that if water flow could be accurately managed, long term treatment in this way would markedly improve the physical stats as well as the Willpower, Spatial Sense and Kinesthetic Sense of the test subjects. Longer trials are required, and better water flow mechanisms must be set in place. The current design requires too much oversight to be effectively automated, though engineers are hard at work to overcome these circumstances.
I will be testing new chambers exploring this avenue of research soon, using controlled flow chambers and static pools in which the subject will have to swim should it wish to attain food, drink, and sleep.