Quiet Coastal Historic Village in Spain other than Nerja?

A short distance north of Barcelona, Begur, in the Costa Brava. Also Tossa de Mar, Cadaques and more.

Though not a village, Malaga is a relaxed, walkable small city with a beautiful historic center, lovely port and beach, good food and welcoming people. We enjoyed it much more than Nerja.

How long do you have? The problem is, Nerja is really out of the way from your Itinerary of Madrid and Vigo. If you really wanted some beach, then I would suggest another route to Porto. Certainly Madrid is fine, but I would suggest then going to Seville, spend a couple days to get some more Spanish flavor, then take a bus to Tavira, on the Southern Portuguese coast. Tavira fits the bill for a smaller town, great beaches accessible by ferry, great restaurants, a Pub plus lots of bars, then from there you can get to Porto by train via Faro and Lisbon, with Lisbon worth a couple days.

YouTube has a bunch of videos on Tavira if you want a look, as well as Seville and Lisbon. All three are also in Rick's guides.

I'd look a the Atlantic coast of Galicia. Many charming towns and the area is much closer/easier to Porto. (People from this region drive to Porto to use its airport.)

-Near Vigo, Pontevedra is an enchanting small city with a population of 80k and was the medieval hub of the region. It's on a river and a couple of miles from the larger bay. The city was a pioneer in limiting cars, and much of the center is delightfully pedestrianized.

-Countless options going up the coast from there, but the historic towns will be truly small and might be hard to spend a week in. Muros and Vilagarcia de Arousa come to mind. There are more modern towns that are tony summer destinations, but they mostly lack charm and will be half-closed up by October.

You may need to make a transportation connection in Vigo, but it's the last place in Galicia I'd want to stay. I've seen a lot of Spain (4-1/2 months there since 2016), and Vigo is the least interesting city I've been to. Pontevedra is much more attractive.

Estepona fits the bill perfectly. I visit pretty much every year at some point and I'll be there again next week (currently further along the coast in Fuengirola). It's a contrast to much of the Costa Del Sol, maintaining much of its Spanish charm.

https://www.visitcostadelsol.com/things-to-do/estepona-p9661

Andalucia to Porto is a logistical challenge. I would perhaps aim for a place on the Portuguese coast (like Viana do Castelo) or on the Galician coast (like Baiona). Sure, you might not be able to swim, but early October should still have decent weather, and the beaches are magnificent.

I too give a nod to Baiona in Galicia. If you decide on it, consider staying at the Parador. It has a great view of the bay and surrounding area and a good place to relax. It does have a pool. The town center is small and doesn’t take long to see. It’s a short walk from the Parador.

We stayed there in September 2023 and it was warm enough to swim. I will say we did have a rental car to get around.