Fertilizer applications are poised to increase across sub-Saharan Africa (SSA), but the fate of added nitrogen (N) is largely unknown. We measured vertical distributions and temporal variations of soil inorganic N following fertilizer application in two maize (Zea mays L.)-growing regions of contrasting soil type. Fertilizer trials were established on a clayey soil in Yala, Kenya, and on a sandy soil in Tumbi, Tanzania, with application rates of 0–200 kg N/ha/yr. Soil profiles were collected (0–400 cm) annually (for three years in Yala and two years in Tumbi) to examine changes in inorganic N pools. Topsoils (0–15 cm) were collected every 3–6 weeks to determine how precipitation and fertilizer management influenced plant-available soil N. Fertilizer management altered soil inorganic N, and there were large differences between sites that were consistent with differences in soil texture. Initial soil N pools were larger in Yala than Tumbi (240 vs. 79 kg/ha). Inorganic N pools did not change in Yala (277 kg/ha), but increased fourfold after cultivation and fertilization in Tumbi (371 kg/ha). Intra-annual variability in NO−3-N concentrations (3–33 μg/g) in Tumbi topsoils strongly suggested that the sandier soils were prone to high leaching losses. Information on soil inorganic N pools and movement through soil profiles can h vulnerability of SSA croplands to N losses and determine best fertilizer management practices as N application rates increase. A better understanding of the vertical and temporal patterns of soil N pools improves our ability to predict the potential environmental effects of a dramatic increase in fertilizer application rates that will accompany the intensification of African croplands.