Local buses for Elounda (€1.90, 20 minutes, 14 daily) leave from stops around town, including the one on Koundourou opposite the tourist office.
The main bus station is about 1.5km north of the city centre. Check www.ktelherlas.gr for the current schedule.
Club Cars Has cars for hire from €50 per day in high season.
The most central taxi rank is behind the tourist office down by the lake. Typical fares are €14 for Elounda, €21 for Plaka, €14 for Kritsa and €18 for Ancient Lato.