As the first bridge to use the deflection theory in its design, the Manhattan Bridge is considered to be the forerunner of modern suspension bridges.

Although a construction contract was awarded in 1901 and preparations were being made to begin work on the new bridge, the mayoral election that fall brought about a change in administration. Gustav Lindenthal, the new Commissioner of the Bridge Department, decided to change the design to use stiffened eye-bar chains to make it more aesthetically pleasing.

The redesign of the suspension bridge and the attempt to use eye bar chains in lieu of wire cables made it the most debated bridge in the technical journals and newspapers of the time, including Transactions of the American Society of Civil Engineers. No such structure of this magnitude had ever been built and new methods of construction would be required along with types of eye-bars that had never been fabricated before. Although in 1903 a panel of prominent engineers selected by Mayor Seth Low and the Art Commission both endorsed Lindenthal's design, he was unable to obtain approval for funding by the Board of Aldermen.

The next mayoral election brought about another change in administration in 1904, which intended to design a new wire cable suspension bridge, as the uncertainties involved in constructing the eye-bar design would likely further delay the opening of the bridge and further increase congestion at the other lower East River crossings.

The Manhattan Bridge pioneered the use "two-dimensional" slender steel towers.

The third design for the Manhattan Bridge—the one that eventually constructed—was the first to use the deflection theory for the stiffening of the deck. Leon Moisseiff, the earliest proponent of this method in the United States, prepared the calculations under the supervision of chief engineer Othniel Foster Nichols. Use of the deflection theory resulted in a much lighter and shallower stiffening truss, reducing the amount of materials that were required in construction.

When the Manhattan Bridge opened on December 31, 1909, it was the third longest suspension bridge in the world with a main span of 1,470 feet (448 m). Its four 21-inch (53 cm) diameter cables were the largest in the world when spun. As the first bridge to use the deflection theory, it is considered to be the forerunner of modern suspension bridges and served as the model for the major suspension bridges built in the first half of the twentieth century. The Manhattan Bridge also pioneered the use "two-dimensional" slender steel towers, which are 322 feet (98 m) high, and was the earliest bridge to incorporate nickel steel to a large extent in construction.

Essentially planned in the horse and buggy era, the Manhattan Bridge originally carried eight railway tracks—four streetcar tracks and four rapid transit tracks. The rapid transit tracks were first intended for elevated trains, but instead they were used by heavier subway trains. The placement of the subway tracks on the outer part of the bridge caused severe torsional stresses, requiring the need for an extensive rehabilitation in the end of the twentieth century. Today, the Manhattan Bridge carries a third of a million passengers in nearly 1,000 subway trains each day, making it the busiest public transit crossing into Manhattan.

The Manhattan Bridge was designated as a National Historic Civil Engineering Landmark by ASCE in 2009, the year of its centennial anniversary. A bronze plaque was installed on the pedestrian walkway at the Brooklyn end of the bridge, near the intersection of Jay Street and Sands Street.