The river originates in the southern part of Maranhão, and drains north into the Baía de São Marcos, an estuary that also receives the Pindaré and Grajaú rivers, which are sometimes considered tributaries of the Mearim.

The Mearim is approximately 800 kilometers long, flowing through the marshlands of the Atlantic Coastal Plain.

It meets the Atlantic Ocean at the Sao Marcos Bay, where it forms a common estuary with another river, Pindare.

The river's upper and middle courses are characterized by rapids.

[1] The river defines the southern boundary of the Tocantins–Araguaia–Maranhão moist forests ecoregion.