It is the largest tributary of the Pasig River, with headwaters in the Sierra Madre Mountains in what was known as Montalban, presently the municipality of Rodriguez, Rizal.

It has a total area of nearly 75.2 hectares (0.752 km2) and is 27 kilometers (17 mi) long.The riverbank has an elevation of 8 meters above sea level at the boundary of San Mateo and Marikina.

[6] Further downstream the Nangka River and its own tributary in the Sapang Labo Creek mark the boundary between San Mateo and Marikina.

Instead, these waterways are linked in a complex network with the Balanti, Halang, and Muntingdilao Creeks and the Sapang Baho River, eventually emptying into the Manggahan Floodway and Laguna de Bay.

Due to neglect and uncontrolled industrial waste, rising pollution of the river had caused alarm that national and local administrations seek to repair.

[9] The Marikina River is on a verge of an ecological imbalance as a strange species of fish has dominated its ecosystem.

[10] A scientific study of the species found in five locations in the Laguna de Bay tributary system, including the Marikina River, revealed that the specimen of janitor fish previously reported as Hypostomus plecostomus actually belongs to the genus Pterygoplichthys, family Loricariidae.

The expressway bridge will be built within the city of Marikina, and will serve as a solution to heavy traffic along the Magsaysay Boulevard-Aurora Boulevard-Marikina-Infanta Highway corridor as well as Ortigas Avenue.

On September 26, 2009, at about 6:00 pm PST, Typhoon Ondoy hit Metro Manila and dumped one month's rainfall in less than 24 hours, causing the Marikina River system, including the Manggahan Floodway, to burst its banks rapidly.

It is believed that blocked pipes, a poorly maintained sewerage system, and uncollected domestic waste were major factors in the speed with which the flood waters engulfed the surrounding area.

This prompted President Gloria Macapagal Arroyo to declare a State of National Calamity and set up a task force to rescue the inhabitants.

Thereafter, efforts have been made to improve the drainage system for the whole city by fixing the sewers and the new trademarked "Red Sidewalks".

On June 24, 2011, heavy rains of Severe Tropical Storm Meari affected Luzon including Metro Manila.

On September 27, 2011, Typhoon Pedring dumped heavy rains like Ondoy over Luzon including Metro Manila and nearby provinces.

Although located hundreds of kilometers away from the Philippines, the southerly flow from Typhoon Haikui in early August 2012 enhanced the southwest monsoon across much of Luzon.

[14] As a result, widespread heavy rains impacted regions still recovering from deadly floods triggered by Typhoon Saola less than a week earlier.

[15] During a 22‑hour span from August 6–7, 687 millimeters (27.0 in) of rain fell in parts of Metro Manila, leading local media to compare the event to Typhoon Ketsana in 2009, which killed 464 in the city.

[22] On July 24, 2024, several areas in Luzon were affected by the heavy rains caused by the strengthening of Typhoon Gaemi and the enhancement of the southwest monsoon.

Initial forecasters said that Typhoon Gaemi would not make landfall in the country but moisture from the storm would be drawn into the southwest monsoon and bring heavy rainfall and strong winds to the archipelago.