It's hard to say, using the lake will cause problems, because it's freshwater and the ocean is salt-water and they'd mix a bit which would disturb some marine communities. Also the increased traffic would disturb those communities. And using the river plan they'd be disturbing more marine communities and the terrestrial communities around the river.
Using the Lake Atlanta plan, they wouldn't distrub the San Juan, but they'd disturb the San Miguelito wetland all the communities along the way, and Lake Atlanta. Due to the distance it would definitely have a big impact.
In Panama they disturbed lots of communities as well.
Proportionally, the Lake Atlanta plan most likely has a bigger environmental impact than the Panama Canal. The San Juan plan is much more mixed, because it mainly affects marine communities and the effect on the river could be pretty big.