Hi rfitts,
First, a careful definition of the fluid requirements may be in order. When you say water based, some folks think 90/10 or water/glycol is "water based". Or do you mean "pure water" systems, eg. no additives at all allowed? You will have difficulty with well meaning salesmen, otherwise. The next primary consideration is whether or not you are going to use a closed loop system.
The nuclear industry is looking at pure water based systems to mitigate consequences of hydraulic spills and ruptures in contaminated areas. Pure water spills in contaminated hot cells just evaporate and do not cause a "mixed waste" problem. Other systems require pure water with dissolved gases such as nitrogen removed as well.
Closed loop, pure water hydraulic systems require continuous or at least periodic monitoring and treatment of the water to prevent small critters from taking up residence. This puts some otherwise strange requirements on the tank reservior such as ultraviolet light sterilizers, etc. Pure water is a relatively poor lubricant so pump/motor/actuator bearing lubrication is not simple. Pure water has low viscosity relative to more common hydraulic fluids so seal performance and wear considerations in pump/motor/valve/actuator are problematic.