In the food-energy-water (FEW) nexus, livestock has a dominant place. It is generally considered as water, energy and land-intensive. Aquaculture could provide additional animal protein and contribute to meeting the food demand. However, aquaculture requires natural resources and causes freshwater pollution due to aquafeed, fertilizer, and hormone use. This study assesses the sustainability of aquaculture using the indicators water footprint (WF), energy footprint (EF) and land footprint (LF), comparing results with livestock. It uses extensive, semi-intensive and intensive Tilapia aquaculture in Mexico as a case study including broodstock, breeding, fattening, processing, and transportation phases. Tilapia production in intensive aquaculture has the largest footprints. Blue WFs are smallest in semi-intensive systems; green WFs, EFs and LFs are smallest for extensive systems. For protein, tilapia from intensive systems has the largest WF (126 l/g protein), beef (51 l/g), pork (33 l/g) and poultry (14 l/g) have smaller WFs. EFs per unit of protein or nutritional energy fall in the range of values for beef, poultry and pork. LFs of Tilapia (m2/kg) are larger than LFs of poultry but fall in the range of beef and pork. Per unit of nutritional energy EFs are similar to EFs for beef but larger than EFs of poultry and pork. From a FEW nexus perspective, it is not more sustainable to replace livestock with Tilapia. Tilapia requires more freshwater than beef, pork and poultry and pollutes larger amounts of water. For energy and land, Tilapia is not the better choice, because footprints are comparable.