This research was published by Elsevier Ltd. in 2022Intensive paddy farming activities involve higher use of irrigation water and agrochemicals to increase crop productivity per unit area. However, a practice may result in environmental challenges due to nutrient loss and agro-chemicals contamination from agricultural fields. The present study characterized the relationship between agricultural soil phosphate (P) status and P levels in water bodies in Usangu agro-ecosystem (UA), the area famous for paddy rice production in Southern Highland Tanzania. The studied soil pH ranged from 6.4 to 7.6, while water pH was 4.9–6.8, which varied among study sites and negatively correlated to each other. This study found a positive correlation between P concentration (P < 0.001, R2 = 0.78) in agricultural soils and water samples in the study area, where P in soil were 1.66–17.56 mg/kg and 0.02–1.65 mg/L in water. This correlation pattern of P in soil and water indicates that increased P content in farming areas under poor management (flooding system of irrigation), as observed in the study area likely to influence increased levels of P in water bodies leading to water eutrophications, but also reducing the land productivity per unit area. The significant P enrichment (>1.65 mg/L) from agricultural fields to water bodies found in different water samples from irrigation schemes potentially leads to eutrophication. To sustainably manage P concentration in water bodies and increase land productivity per unit area, the hotspot for P loss to water bodies in the agro-ecosystem has to be identified and managed, but also flooding irrigation system standard in the study area has to be abandoned to reduce plant nutrient loss and contamination of water bodies.