Irrigation has contributed significantly to poverty alleviation and food security; however, the sustainability of irrigated agriculture is being questioned both economically and environmentally. Agriculture is the economic sector where most water is consumed, but the lowest price is practised. This article presents an interdisciplinary approach to selecting and prioritizing infrastructure, by differentiating water sources for irrigation, in the case of two complex irrigation systems. Comparative analysis was undertaken for major hydrological, hydraulic, hydrotechnical and economic parameters in order to estimate a long-term water supply for irrigation. In the case of complex irrigation water supply systems, differentiating the ‘subsystems’ per water source and allowing their separate development require less investment and give a better chance for the project implementation. The average calculated investments in basic irrigation infrastructure were in a wide range, from EUR3327 to 10,103 ha−1, depending on anticipated water source (impoundments, groundwater and rivers). Economic water price also varied widely, EUR0.09–0.30 m−3, depending on the water source for irrigation.