Hey great post!
1. You need to do some calculations for the stability of your boat. Your mass will change considerably when you fill in water in your containers. So the placement of your mechanism will differ as well the overall boat design. The first step is to design how much water sample will you collect. Perhaps 200 ml per sample? Also lowering down that mechanism will also tilt your boat if not calculated.
2. Another way to fill in your sample bottles is control the lid using a solenoid valve. I have these goodies in my office if you are interested.
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