Protecting groundwater from nitrogen contamination such as soluble NO₃-N is an important public health concern and a major national environmental issue in Egypt. The objective of this study was to determine and monitor the influences of bio-spent grain and mineral fertilizers on levels of nitrate leaching and other forms of nitrogen contamination in agricultural wastewater for controlling nitrogen pollution and protecting groundwater safety. Spent grain organic wastes has no value and is available at no cost all year from the beer industry. Eight treatments were established, including spent grain (S2, 20 g kg^-1 soil); compost (M2, 20 g kg^-1 soil); mix compost with spent grain (M1S1); Azospirillium sp., inoculation (A1); inoculation A1 with S2, (A1S2); inoculation A1 with M2, (A1M2); nitrogen fertilizer (NF), and control (CK, no fertilizer). All treatments were mixed with 30 kg soil pots under greenhouse conditions, Zea mayz L. seeds were planted in the soil pots. The most relevant nitrogen leaching forms were collected and analysed every month for four months. The soil drainage was collected under the pots by closed system. The bio-spent grain application effectively increased soil organic matter content, plant nutrients, germination rate, and reduced agricultural wastewater pollution. The Ca²⁺, K^-1 and Na^-1 cations in the leaching were not stable, but were present at high levels. Total N, NO₃ ^-, NH₄ ⁺ and Cl^- were significantly lower in S2, A1, and A1S2 treatments than in NF, M2 and control treatments. The agricultural wastewater in most menial fertilizer's treatments belonged to class III and IV in the Egyptian water standard, which defines water that is unsuitable for human consumption. Our health risk assessments showed that NO₃ ^--N posed the greatest carcinogenic risk. Therefore, using A1S2 as bio-organic fertilizer reduces the risks of soluble NO₃ ^--N in agricultural wastewater.