Water has economic and ecological significance. However, quality deterioration due to salinity causes significant decrease in agricultural productivity and a public health problem. This study focuses on hydro-chemical and microbial quality of water sources in Kilifi County. Water samples were collected from 25 different locations within Kilifi County and indicators of salinity and microbial load analyzed. Temperature, pH, EC and TDS were determined using portable pH meter. Anions; F-, Br-, Cl-, SO42-, PO43-, NO2-, NO3-, CO32-, HCO3- and NH4+ were determined using Ion Exchange Chromatography. Cations; Na+, K+, Ca2+, Mg2+, Zn2+, Fe2+, Cd2+, Cr3+, Al3+ and Ag+ were determined using flame photometry. Standard methods were used to determine Microbial loads. Results were pH (7.42±0.52), Temperature (24.61±0.21oC), EC (3.44±0.75 dscm-1), TDS (1672.53±122.87 mgL-1) and Turbidity (152.29±41.20 NTU). Anions; F- (2.90±0.24 mg/L), Cl- (1756.68±900.50 mg/L), NO2- (4.47±0.49 mg/L), Br- (11.72±1.20 mg/L), NO3- (4.67±0.38 mg/L), HCO3- (200.54±25.58 mg/L) PO43- (0.94±0.10 mg/L), CO32- (29.94±2.32 mg/L), and SO42- (300.64±42.47 mg/L). Cations; K+ (8751.80±214.04 mgL-1), Na+ (59.43±1.98 mgL-1), Ca2+ (4.00±0.16 mgL-1), Mg2+ (59.43±1.98 mgL-1), Zn2+ (0.76±0.30 mgL-1), Cu2+ (0.18±0.01 mgL-1), Ag+ (0.03±0.01 mg/L), Cd2+ (0.07±0.01 mg/L), Cr3+ (0.35±0.01 mg/L), Al3+ (0.33±0.01 mg/L) and NH4+ (2.01±1.96 mg/L). Microbial load; MPN (20811.00±402.00), Total coliforms (2970.00±60.00 CFU 100 mL-1), E. coli (26.00±3.00 CFU 100mL-1), S. aureus (411.00±12.00 CFU 100mL-1), Shegela (24.00±2.00 CFU 100mL-1) and S. typhi (67.00±2.00 CFU 100mL-1). Temperature, pH, EC, TDS, Turbidity, F-, Cl-, Br-, PO43-, Na+, Zn2+, Fe2+ and microbial load were above WHO limits whereas SO42-, NO2-, NO3-, CO32-, HCO3-, NH4+, K+, Ca2+, Mg2+, Cd2+, Cr3+, Al3+ and Ag+ were below WHO limits. The study concludes that water sources in Kilifi County are unsuitable for domestic and agricultural uses. It’s recommended that a continuous water quality monitoring program be put in place and development of effective management practices for utilization of the surface water resources be instituted.