Almost all of Manila sits on top of centuries of prehistoric alluvial deposits built by the waters of the Pasig and on some land reclaimed from Manila Bay . Manila 's land has been altered substantially by human intervention , with considerable land reclamation along the waterfronts since the American colonial times . Some of the natural variations in topography have been evened out due to the urbanization of the city . As of 2013 , Manila has a total area of 42 @.@ 88 square kilometres ( 16 @.@ 56 sq mi ) .