Phuleli, a non-perennial canal, was constructed in 1955 with design discharge capacity of 15000 cusec to meet the irrigation water requirements of left bank districts of lower Sindh. The canal originates from Ghulam Muhammad Barrage (Kotri Barrage) on the left bank of river Indus and passes through Hyderabad, the second largest city of Sindh province. The canal water is mainly used for irrigation purpose; however cities and villages in its command also draw water for the domestic use. Highly toxic effluent from plastic factories, illegal cattle pens, slaughterhouses and municipal sewage water are directly discharged into the Phuleli Canal when it passes through Hyderabad city which has deteriorated the canal water quality and thus has put lives of millions of people at risk. Present study was thus conducted to investigate the effect of disposal of untreated domestic and industrial sewage water and waste into Phuleli Canal on its water quality and subsequent effect on groundwater and soil properties in its command area. In the study, the quality of the canal and groundwater was monitored through sampling around the year for four seasons (summer, autumn, winter, and spring) at seven different locations (RD-0, RD- 30, RD-50, RD-70, RD-90, RD-110 and RD-130) along Phuleli Canal. The soil physico-chemical properties at various soil depths (0-20, 20-40 and 40-60 cm) and at different locations in the canal command area were also determined. The results of the study revealed that EC, HCO3 , Cl , SO4, Ca+Mg, Na, SAR, Cd, Cr, Pb and As of canal water increased considerably towards down-reach (RD-130) of canal during winter season with the exception of Zn, Fe, pH and K showing maximum at up-reach (RD-0) and decreasing trend towards down-reach. Cu concentration was high towards down-reach (RD-130) during spring season and Mn was high at up-reach (RD-30) in summer. The groundwater of canal command area had higher EC, HCO3, Cl, Ca+Mg, Na, SAR, Cd, Cr, Pb and As and in the down- reach (RD-130) during winter. The pH and K had opposite trend, being high pH near up-reach (RD-0) during summer and low towards down-reach (RD-130) during autumn. Zn was high towards up-reach (RD-0) during winter season and it relatively decreased towards down-reach (RD-130) during summer season. Fe concentration was greater in groundwater at up-reach (RD-30 and RD-50) during winter. Cu concentration was maximum towards down-reach (RD-130) during summer season. In soils irrigated by Phuleli Canal, high soil EC, Cl, Ca+Mg and Na were found near soil surface (0-20 cm) during winter near down-reach (RD-130). However, they were found low in the soil depth 20-60 cm during summer near up-reach (RD-0) in canal command area. The soil HCO3 was high in the layer near to soil surface (0-20 cm) during winter in up-reach (RD-0), whereas, it decreased in the lower soil depth during summer towards mid to down reach. The soil SO4 increased in upper soil layer (0-20 cm) during autumn season in down-reach (RD-130). Soluble K was greater in upper soil surface (0-20 cm) during summer in up-reach (RD-0) and decreased towards down-reach (RD-130) in lower soil depth (40-60 cm) during summer in down reach (RD-130). Zn and Fe contents were high in upper soil surface (0-20 cm) during winter in up-reach (RD-0 and RD-30) decreased in lower soil depths (20-40 cm) in down- reach (RD-130) during summer. Cu content was high in upper soil layer (0-20 cm) near down-reach (RD-130) during summer and decreased in lower soil depths (40-60 cm) near up-reach (RD-0) during winter season. Cd, Cr, Pb and As content were higher in upper soil layer (0-20 cm) near down-reach (RD-130) during winter and decreased in lower soil depth towards down-reach (RD-130) during summer. The ions concentration of Phuleli Canal water was within the permissible limits given by WHO and FAO for human consumption and agriculture purpose respectively in all seasons and at all locations. However, Fe, Cd and Cr concentration in water were higher than WHO permissible limits and Cu and Mn greater than FAO permissible limit at down-reach. The ions concentration of CO3, HCO3, Cl, SO4, Ca+Mg, and pH of groundwater were within the permissible limits except for EC that was higher than the reference value set by WHO and FAO; while the ions concentration of Cl and Na, SO4 and K were beyond the permissible limits set by WHO for human consumption in all season at all sampling locations. Fe, Cd, Cr and Pb concentraton in groundwater were higher than WHO permissible limits while Cu and Mn concentration greater than FAO permissible limits. EC, Zn, Fe, Cu, Mn, Cd, Cr and Pb of soil in surface layer were greater than FAO permissible limits. Heavy metals concentration/content in canal, groundwater and soil water samples were found higher in down-reach compared to the up-reach which may be due to the discharge of untreated industrial waste into canal. The present study concludes that due to continuous disposal of untreated effluent wastewater into the Phuleli Canal from different sources most of the canal and groundwater samples contained highly toxic metals above the permissible limits set by WHO and FAO for human and crop consumption respectively. The water contamination was greater during the winter season due to low water discharge from Kotri Barrage into canal and reception of low rainfall in the area. Because of accumulation of trace and heavy metals in soils of Phuleli Canal Command area, the crops and vegetables grown might not be suitable for human and animal consumption. To maintain canal water quality within permissible limits, it is suggested that (i) industries must be compelled to discontinue draining toxic effluents in the canal, (ii) municipal sewage water, after treatment, should be used directly for urban agriculture instead of discharging into waterways, (iii) illegal pens and slaughter houses be discouraged to pour their waste into the canal, (iv) government must install water treatment plants for regular supply of drinking water for the people living alongside the canal, (v) the canal water quality should be regularly monitored and (vi) awareness programs should be initiated to provide knowledge to the people about the polluted water, associated health risks, and its safe use.