I was doing some reading about the Battle of Brest in WWII during Operation Overlord and it became clear that taking port cities to supply the Allied armies was a key goal, though the article focused on the battles more than the logistics. Which ports handled the bulk of the supply traffic? How did the Allies move enough materiel through France to support such an enormous army? How successful were the Germans in destroying ports to prevent this?
Logistics were always a key factor in the planning of Overlord. Prior experience showed that capturing ports was difficult as they were a natural focus for defensive efforts, and once captured extensive work would likely be needed to repair sabotage and demolitions carried out by the defenders. Supplies would therefore have to come over the beaches initially, assisted by the artificial Mulberry harbours, until sufficient ports could be taken and cleared. An initial plan was for US forces to have Cherbourg operating by D+11, with a push into Brittany to take Brest and construct a new facility in Quiberon Bay around D+54. (Figures from Logistical Support of the Armies: May 1941 - September 1944, Roland G. Ruppenthal).
As it was Cherbourg only fell at the end of June, and rather than three days it took three weeks for the port to be cleared; Col. Alvin G. Viney described the damage done to the port as "... a masterful job, beyond a doubt the most complete, intensive, and best-planned demolition in history." (Cross-Channel Attack, Gordon A. Harrison). The majority of supplies therefore came over the beaches until August when Cherbourg was fully operational, some minor Normandy ports were opened, and Operation Dragoon started to make southern French ports available. The beaches remained in use, though with less traffic as weather worsened, and as the Allies pushed east along the channel coast heavily fortified ports such as Le Havre and Rouen were besieged, captured and repaired.
After initial slow progress, behind initial estimates, the breakout from Normandy happened far quicker than expected; by mid-September, about three months into the campaign, Allied forces were reaching objectives they were only planning to capture after a year. Antwerp was captured at the start of September with its docks intact but could not be utilised until the Scheldt estuary had been cleared, which only happened in November, Market Garden proving something of a distraction in the meantime. Ports in Brittany were scarcely used, with Brest heavily damaged and the planned facility in Quiberon Bay not built; by 1945 Antwerp and the Southern French ports were handling about half the supplies being landed, the rest coming into Cherbourg, Le Havre, Rouen and Ghent (Figures from Logistical Support of the Armies: September 1944 - May 1945, Roland G. Ruppenthal).
Of course the supplies had to get to the front line after being landed, and the unexpectedly rapid advance caused major logistical headaches. The French railway system had been heavily targeted by the Allied air forces in the run-up to Overlord to prevent German reinforcements being rapidly deployed, and though plans were in place to reconstruct it these could not keep up with the speed of advance. Improvisation was therefore required, primarily in the form of truck convoys; the most famous route for these was the Red Ball Express from Cherbourg, though others including the White Ball from Le Havre and the ABC from Antwerp were also established.
For further reading Ruppenthal's Logistical Support of the Armies is available online ([Volume I] (http://www.ibiblio.org/hyperwar/USA/USA-E-Logistics1/index.html) and [Volume II] (http://www.ibiblio.org/hyperwar/USA/USA-E-Logistics2/index.html)), the planning and execution of Overlord being a major theme.
Most of the goods were shipped in to France. By 1944 German Naval power was not what it used to be and while there were still attacks on supply convoys the Allies did a decent job of establishing Naval dominance. As they moved forward they also established supply bases on the mainland so as not to stretch supply lines as well as massive logistic backing behind each unit. Especially interesting is their concept of airborne units where the entire unit staff is dropped with supplies.
There's a very good book about the history of military logistics by Martin van Creveld called Supplying War if your interested in that (https://www.amazon.com/Supplying-War-Logistics-Wallenstein-Patton/dp/0521546575).