If you are in an apartment overlooking the Marina itself, there will be no direct effect from the work.
However, I would advise being prepared, even at night, to walk into the town town rather than drive as there is a massive shortage of parking.
Be aware that it you want to go to the upper town, Luz, Porto de Mos and or all points west of Lagos by car, it is currently better to go via the Seagulls' swimming bath on the roundabout at the entrance to town, the Modelo supermarket and the "Chairs" roundabout rather than going through town on the Avenida.
