Sugarcane is an economic crop and one of the most dominant crops worldwide. This research aim was to evaluate impacts of long-term sugar cane monoculture on some groundwater physicochemical and biological properties as indicators of water quality. Survey study covering sugar belt area of El-Minia Governorate, Egypt was conducted. This study revealed that suitability of groundwater for irrigation falls under the degree of "severe" use restriction, and continuous use of this groundwater for irrigation may increase the salinity problem in the alluvial soils. Groundwater was highly contaminated by total coliforms, E. coli and faecal coliform bacteria under both sugar cane monoculture and crop rotation agricultural systems. The total coliforms population ranged from 360 to 362,Cfu/100 mL, the fecal coliforms population ranged from 212 to 215 Cfu/100 mL and the E. coli population ranged from 248 to 256 Cfu/100mL with insignificant differences between both agricultural systems. Under sugarcane monoculture, average concentrations of cadmium, chromium, nickel and lead in groundwater was 60, 1220, 1320, and 1250 μg/L, while the average concentrations of cadmium, chromium, nickel and lead were 57, 1220, 1350, 1230 μg/L under crop rotation with insignificant differences. The mean concentration of heavy metals observed in groundwater samples often exceeded the permissible limits for irrigation water specified by the World Health Organization (WHO). Based on these findings, it can be inferred that sugarcane monoculture has greatly degraded the quality of groundwater characteristics. This highlights the pressing need for implementing more sustainable management strategies to safeguard groundwater quality in the Nile Valley.