A pot experiment was conducted to study the effects of conjunctive use of saline and fresh water on the growth and biomass of cotton crop and to observe varietal variability for salinity tolerance and ion contents of cotton genotypes. Four cotton genotypes (Sindh-1, BT-121, CRISS-494, CRISS-588) were irrigated with four treatments, C1 (control+ tape water), C2 (EC 4.0 dS m-1, throughout growth period), ( (six irrigation with C2 + six irrigation with C1), C3 (EC 8.0 dS m-1, throughout growth period), (six irrigation C1+ six irrigation C3), (six irrigation C3+ six irrigation C1), C4 (EC 12.0 dS m-1, throughout growth period), (six irrigation C1+ six irrigation C4). The results showed that highest fresh biomass, plant height, number of leaves plant-1, number of bolls and boll weight was obtained in the treatment where tape water was used. Whereas, these parameters were decrease significantly with the increasing salinity levels from 4 to 12 dS m-1 and when saline water was applied continuously throughout growth period. The cotton genotypes Sindh-1 and Bt-21 performed well under conjunctive use of saline and fresh water with maximum values in compare to genotypes CRIS 494 and 588. The Na+ and Cl- accumulation in cotton leaves and in soil significantly increased with rising EC levels of irrigation water. However, Na+ and Cl- contents were found more in CRIS 494 and CRIS 588 than Sindh-1 and Bt1. It is concluded that Sindh-1 and Bt-121 may be cultivated in saline areas with alternate irrigation.