Most of the lagunas south of Montpellier are nice spots in late summer and autumn (Etang de l'Or and Marais de Tartuguière, Etang de Perols, Etang de Maguelone, nature reserve of l'Estagnol...). Great Bustards can be found near the airport (Fréjorgues) but the best time is in winter to see them. A bit further, the Etang de Thau, near Sète, is also a nice spot for flamingos and seabirds. Some of the last French pairs of Lesser grey shrike breed around Villeveyrac and Montagnac and usually leave in late August. A large number of Lesser Kestrels nest and gather for migration, sometimes until September, on the "causse" of Aumelas. Not sure they will still be there though!
Further south, the Etangs de Narbonne also host a lot of Mediterranean and migrating birds at that time of year (link below for a map).
I also found other spots on birdwatching blogs (links below).