Aquaponics (AP) is a food production system that combines hydroponic (HP) crop production with recirculating aquaculture. Different types of hydroponic systems have been used for growing crops in aquaponics. However, very few studies have compared their suitability and efficiency in an aquaponic context. The study presented here compares tomato yield, morphological (external) and biochemical (internal) fruit quality, and overall tomato plant vitality from three different HP systems (nutrient film technique, drip irrigation system, and floating raft culture) and examines the distribution of nutrients in different parts of the tomato plant. Three replicate AP systems were set up, each incorporating the three different HP systems coupled with a separate recirculating aquaculture unit growing Nile tilapia. The results showed that the choice of the cultivation system had little influence on most of the above-mentioned properties. Tomato fruit mineral content was found to be in similar range for N, P, K, Ca, Mg, Fe, and Zn as reported in the literature. Yield and fruit quality were similar in all three systems. However, the drip irrigation system did perform slightly better. The slightly higher oxygen radical absorbance capacity (ORAC) of the fruits grown in AP in comparison to commercially produced and supermarket derived tomatoes might indicate a potential for producing fruits with higher health value for humans.