Funds for capital outlay are for the construction of irrigation projects and appropriated annually in the General Appropriations Act (GAA). The national government provides local counterpart funds for project implementation.

Project funds also have foreign exchange component from loans and grants. The foreign financing institutions which have extended loans or grants to NIA are the International Bank for Reconstruction and Development (The World Bank), Asian Development Bank, Japan International Cooperation Agency, China National Construction and Agricultural Machinery Import and Export Corporation, United States Agency for International Development, International Fund for Agricultural Development, Organization of Petroleum Exporting Countries, International Development Association, Philippine Australian Development Assistance Program. Foreign exchange allocations are also included in the annual GAA.

NIA is authorized to keep its corporate earnings from various activities. Such internally generated funds are used mainly for operation and maintenance, repair and maintenance of equipment, institutional development, and investigation and survey. These include irrigation service fee (ISF) collection, equipment rentals and pump amortizations categorized under operating income, and administration and engineering overhead charge, interest income, proceeds from the sale of idle assets and communal irrigation projects and systems amortizations as non-operating income. NIA is authorized to charge five percent (5%) of the total costs of the projects it implements as administration and engineering overhead charge or management fee.

May dalawang uri ng pondo ang NIA:

Capital Outlay na nakabadyet sa taunang General Appropriations Act Current Operating Budget na sariling kinikita.

Ang mga pondo para sa capital outlay ay para sa pagtatayo ng mga irrigation project at inilalaan kada taon sa General Appropriations Act (GAA). Nagbibigay ang national government ng local counterpart fund para sa pagpapatupad ng proyekto.

Ang mga pondo ng proyekto ay mayroon ding foreign exchange component mula sa mga loan at grant. Ang mga foreign financing institution na nagbigay ng loan o grant sa NIA ay ang International Bank for Reconstruction and Development (The World Bank), Asian Development Bank, Japan International Cooperation Agency, China National Construction and Agricultural Machinery Import and Export Corporation, United States Agency for International Development, International Fund for Agricultural Development, Organization of Petroleum Exporting Countries, International Development Association, Philippine Australian Development Assistance Program. Kasama rin sa taunang GAA ang mga foreign exchange allocation.

Pinapayagan ang NIA na panatilihin ang kinikita nito mula sa iba't ibang gawain. Ang mga sariling kinikitang pondo ay ginagamit pangunahin para sa operasyon at maintenance, pagkukumpuni at maintenance ng mga equipment, institutional development, at imbestigasyon at survey. Kabilang dito ang koleksyon ng irrigation service fee (ISF), renta ng equipment at pump amortization na nasa ilalim ng operating income, at administration at engineering overhead charge, interest income, kita mula sa pagbebenta ng mga hindi ginagamit na asset at amortization ng mga communal irrigation project at system bilang non-operating income. Pinapayagan ang NIA na maningil ng limang porsyento (5%) ng kabuuang halaga ng mga proyektong ipinatutupad nito bilang administration at engineering overhead charge o management fee.