The Decentralised Wastewater Treatment System (DEWATS) provides low cost onsite sanitation to residents living in informal settlements. Wastewater management through agriculture prevents environmental pollution and promotes sustainable agriculture. This study investigated the effects of fertigation with DEWATS effluent to field capacity in three South African soils under a banana crop. The experiment was conducted as a complete randomised design in a greenhouse with two irrigation water treatments (DEWATS effluent vs municipal tap water irrigation + fertiliser) × three soil types (Ia, Cf and Se) and four replicates over 728 days. Data was collected on crop growth, nitrogen (N) and phosphorus (P) uptake and dynamics in the soil. The DEWATS effluent significantly (p < 0.05) increased N and P uptake and soil NH+4-N and extractable P concentrations. Furthermore, DEWATS effluent fertigation significantly (p < 0.05) increased N leaching from the Ia soil and P leaching from the Cf soil. Nitrogen and phosphorus leaching from DEWATS was lower than the tap water irrigation + fertiliser treatment. There was, however, excess N and P accumulation from the DEWATS than the irrigation + fertiliser treatment, which would cause environmental concerns from runoff and leaching losses in the medium to long-term.