Lowland rice production in sub-Saharan Africa (SSA) is often limited by water supply and low phosphorus (P) availability and efforts are needed towards more efficient management of both resources. Field and pot experiments were set up to evaluate combinations of water saving technologies and micro-dose P placement methods (i.e. the localized application of a small P dose to a sub-surface area, often combined with seeds into the planting hole) with due attention to treatment effects on root architecture. A two-year field experiment was set up in a lowland rice field in Tanzania with factorial combinations of different levels of water supply (field capacity, alternating wetting drying, permanent flooding) and P application (no P; 3.45 and 6.90 kg ha−1 placement versus 25 kg ha−1 broadcast), thereby testing residual effects in year 2. A trial in pots (10.5 L) was additionally performed with equivalent treatments and allowing measurements of soil solution composition, apparent fertilizer efficiency, and root density versus depth. Rice grain yields ranged 0–5 ton ha−1 and mainly responded to P application. The P placement at the lowest P rate resulted in higher grain yield at field capacity (2.0–2.5 ton ha−1) than in flooded rice (1.2–1.6 ton ha−1), whereas these differences were absent at higher P rates. Lower water supply at field capacity enhanced root growth and rooting depth, decreased nodal root thickness and enhanced root P uptake efficiency compared to flooded condition. Modelling P diffusion outwards the granules showed more restricted P diffusion under reduced water supply and, therefore, less P immobilization in the soil under field capacity. These differences between water treatments were more pronounced at lower than at higher P supply. This study shows that both root responses and P diffusion outwards placed granules explain rice development and yields under micro-dose P placement and water saving technologies. P placement can contribute to intensify rice production while countering soil P decline in P deficient lowlands when resources are limited.