The expansion of food production is getting more important due to a rising world population, which is relying on food security on a regional and local scale. Intensive food production systems create a negative impact on the regional ecosystem because of agrochemical pollution and nutrient rich water discharges into nearby rivers. Furthermore, these systems are highly depending on regional water resources causing water scarcity and soil erosion due to the overexploitation of natural resources in general. The objective of this article is to review the water usage in the two most water intensive food production systems, agriculture and aquaculture showing lacking areas, like system management and climate change, which must be considered in the implementation of sustainable water footprint. In addition, the review includes an analysis if the combination of both production system into aquaponic food production and the possibilities of water saving. There are a variety of water footprint analyses for crop and aquatic animal production, but there is also a lack of information about the system management including irrigation systems, system cleaning processes, water substitution, pond removal, evaporation due to climate change and especially in aquaculture, the water footprint of industrial elaborated fish feed.