Waldronville is located close to the Kaikorai Lagoon, an expanse of water at the mouth of the Kaikorai Stream protected from the ocean by a sandbar which stretches inland almost as far as the Dunedin suburb of Green Island, 3 kilometres (1.9 mi) to the north. The lagoon is part of a research project aimed at establishing a national estuarine monitoring protocol. The actual island which shares the suburb's name lies 2 kilometres (1.2 mi) offshore to the south of Waldronville. The Island Park Recreation Reserve is a protected are between the village and coast.
The rocky outcrop of Blackhead is located to the east of Waldronville. A major quarry is located at black Head, mining basalt for road metal. There are hexagonal basalt columns at Black head, similar to those further to the east at Second Beach, New Zealand.
Many of Waldronville's streets are named after World War II-era aircraft. The settlement is connected to Brighton and Taieri Mouth to the southwest via a coastal road; in the other direction the road stretches to Green Island. A narrow rural road runs past the quarry and on past Tunnel Beach, connecting with Dunedin's main suburban street system at Corstorphine.
Dunedin's only permanent motor racing circuit, Beachlands Speedway, is located close to the southern end of Waldronville.