Makrigialos lies on the southeastern coast of Crete, about 23 km east of Ierapetra and 58 km southeast of Agios Nikolaos. The original settlement grew up around the small harbour. Further east lies Analipsi, which belongs to the municipality of Sitia, while Makrigialos belongs to the municipality of Ierapetra. As the two settlements expanded, particularly from the 1950s onwards, they grew into a continuous stretch of development along the coast.

Makrigialos Beach stretches east from the harbour. The long sandy beach that gave the village its name usually has shallow water. Taverns and shops line the waterfront, and fishing boats moor in the small harbour.

Two archaeological sites lie close to the shore. At Plakakia, west of the village, excavations uncovered the remains of a Minoan villa from the Neopalatial period. At Katovigli, above the harbour, stands the Roman villa discovered in 1977. Parts of its baths survive, along with the mosaic floor at the entrance.

Inland, Pefki Gorge descends from the village of Pefki towards Aspros Potamos, between pine-covered slopes and past old watermills. Orino Gorge lies to the west. To the east, in the direction of Goudouras, Kapsas Monastery stands on a hillside above the south coast.