It is approximately 100 km (62 mi) long and has had in pre-history jökulhlaups which would be potentially catastrophic, if a similar sized one was to happen in the future.

It flows through narrow gorges in the mountainous area between the glaciers Tindfjallajökull and Torfajökull (and Kaldaklofsjökull), which are also sources, then spreads in the wide Markarfljótsaurar sandur plains at Iceland's south coast, near Þórsmörk.

[2] One of the Markarfljót's tributaries is the river Krossá [ˈkʰrɔsːˌauː], flowing through Þórsmörk, which is notorious for sudden changes in its water level.

[3]: 17  Prehistoric jökulhlaup discharges have been much higher than recently and completely covered the Markarfljótsaurar outwash plain which means the total river basin of about 830 km2 (320 sq mi) with a population of over 1000 is at risk from a jökulhlaup of over 180,000 km3/s (2,600,000 cu mi/min) in size.

[3]: 20 The first bridge over the river was opened in 1934 near Litli Dímon [ˈlɪhtla ˈtiːˌmɔːn].