As a rule, if you're playing Cybran and there's water on the map, you need to build a navy. Use your scouting to make sure you don't over-invest, but if for some reason you don't already have a competent navy then it's a weak spot you can't compensate for. You can't build amphibious units to chase boats off while you establish your own counter-navy. You can't chase hover units with your own factory units.
Just build a navy. You have to. Do it ESPECIALLY if the opponent plays UEF, because there is no other real Cybran counter to Governors beneath a Bulwark. If they build those two boats and you don't have boats of your own, make your final push, and if you don't win then just GG and cntrl-k. The tac missile spam will otherwise carve away your base piece by piece and there's nothing you can do because TMDs get overwhelmed and the cost of air-spamming a Bulwark/Governor combo to death is astronomical.
Cybran is at a disadvantage on mixed maps with water. Having a navy isn't optional for you like it can be for other factions. It's been this way for a long time now and people generally don't acknowledge it as a problem in the grand scheme - or if they do, they don't acknowledge it as a thing that needs thinking about because "Cybran is already too good". It's similar to the problem of how Cybran air factories are slower to produce engineers. It generally pigeonholes Cybran into going land factory first every game, but most players give it a pass even though it's a bit bizarre and the reasoning for it could be debated.