If a hydraulic system becomes contaminated with water or anything else, it has to be completely disassembled and ALL components drained and flushed. This means the tank, the cylinders, the valves, all hoses and tubes (all opened up, cleaned, and reassembled), and the filters and their housings of course.
This is the only way to be sure you have removed all the contaminant. Doing anything else only continues to contaminate, and wastes the new fluid you install. Just draining the tank and changing the filters only dilutes the contamination down to smaller levels every time. There will still be water left in the oil and it will do damage to your system.
Even after a complete system rebuild, the fluid and filters should be changed again after a short interval.
Fluid sampling can help determine what the water level is and you can make some decisions after knowing what that is.
Good luck!