This study aimed to investigate an integrated system that can deal with different pharmaceutical wastewaters. Pharmaceutical wastewater was subjected to biological, chemical and advanced oxidation according to its pollutant’s nature. Wastewater with high total suspended solids (TSS 480 mg/L) was subjected to a conventional chemical treatment process utilizing different coagulants. The best results were obtained by using calcium oxide and alum added with calcium oxide where the removal efficiency of COD was 46.8% and 51%. Highly loaded pharmaceutical wastewater (COD 9700 mg/L, BOD/COD 0.16) had been subjected to Fenton oxidation, the removal of COD reached 80.4%, and the ratio of BOD/COD is enhanced to 0.6. Photocatalysis by using different nanomaterials was applied to pharmaceutical wastewater containing 10 mg/L of phenols. Phenol is completely removed by using mesoporous TiO2 after 90-min irradiation and after 120 min in the case of TiO2/P25 and TiO2/UV 100 nanocomposites, while it is removed by 40% in case of using mesoporous TiO2/Ta2O5. Effluent-treated water from previous routes was subjected to biological treatment and followed with disinfection by using UV as post-treatment. The final COD was 40, and it matches with the Egyptian practice code for water reuse in agriculture (ECP 501 in Egyptian code of practice for the use of treated municipal wastewater for agricultural purposes. The ministry of Housing Utilities and Urban Communities., n.d. No title, 2015). Results showed also using treated wastewater in irrigation of barley and bean seeds achieved germination ratio up to 71% in barely and 70% in bean compared with that irrigated with Nile water, which reached 70% and 75%, while it was about 16.6% and 30% in case of irrigation with untreated wastewater (Jeong et al. in Water (Switzerland). 10.3390/w8040169, 2016).