Lagos by far has the better beaches. For starters they are a lot closer to town and there are several beach resorts you can stay at in the area too. Whilst Faro does have some popular beaches the prettier of the two is definitely Lagos.
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The walk is easily accessible from Lagos town and leads to several beaches and viewpoints along the way. Hiking along the coastline in Lagos was one of my favourite memories of my two week holiday in Portugal, and I highly recommend taking your own coastal walk when you visit Lagos.
And Lagos to Faro railway is a great way to see it all for yourself. But beautiful nature is far from being the only reason to opt for Lagos - Faro train ride. The cities are served by high-speed Alfa Pendular train, providing amazing onboard amenities and boasting incredibly short travel times.
Lagos has a beautiful old town with many restaurants, cafe's, shops and surf schools and many beaches nearby the town centre. There is lots to do in this beautiful beach town. If you stay close to the the town centre everything you need is within walking distance and you don't need to rent a car.