As human population size continues to increase while climate change effects worsen, future food security has become a primary concern for agricultural industries worldwide. Yields of traditional agricultural farming are commonly limited by water and nutrient availability and many crop yields are predicted to decline. Alternative farming practices like aquaponics, which can alleviate these negative yield pressures, may become critical to reaching food production targets. Aquaponics is the cyclic joint production of fish and hydroponic plants where the fish efflux provides nutrients to plants that then purify the water to be recycled to the fish tanks. Here, we investigated acclimation of physiology and functional traits of plants grown in aquaponics versus soil for three leafy green crop species. We compared gas exchange, stomatal anatomy, water use efficiency, and foliar chemistry on newly formed leaves across weekly measurement campaigns. Increased photosynthetic rate, driven by higher stomatal conductance and increases in tissue nitrogen, led to higher harvested biomass in aquaponics for all species. Aquaponics plants adjusted stomatal behavior and to a lesser degree stomatal anatomy to become less water use efficient than plants grown in soil. Collectively, our findings demonstrate the ability of crops to acclimate quickly to aquaponics growing systems that largely remove water and nutrient limitations to plant growth. The increased biomass yield of aquaponics plants compared to soil-grown plants highlights the potential of small-scale aquaponics systems as an efficient and sustainable alternative farming practice.