Salinity magnitude changes are a critical factor for determining the chemistry of natural water bodies and biological processes. Label-free refractive index sensors are promising devices for detecting these changes. A polymer optical fiber (POF) sensor modified with cladding treatment and a bi-layer zinc oxide/silver (ZnO/Ag) nanostructure coating to determine sodium chloride concentration changes through refractive index variations in water is experimentally demonstrated. The use of three ZnO nanostructure shapes, nanoparticles and horizontally and vertically oriented nanorods, as an external layer and a broad spectrum light source from the visible (Vis) to the near infrared (NIR) region are investigated to achieve optimum sensitivity. The rms roughness, optical band-gap and zeta potential (ZP) value for the vertically oriented sample are 148 nm, 3.19 eV and 5.96 mV, respectively. In the NIR region the wavelength-intensity sensitivity values of probes coated with ZnO nanoparticles and horizontally and vertically oriented nanorods are 104 nm RIU-1-12 dB RIU-1, 63 nm RIU-1-10 dB RIU-1 and 146 nm RIU-1-22 dB RIU-1, respectively, and in the Vis area the values are 65 nm RIU-1-14 dB RIU-1, 58 nm RIU-1-11 dB RIU-1 and 89 nm RIU-1-23 dB RIU-1, respectively. The maximum amplitude sensitivity is obtained for the probe coated with vertically aligned ZnO nanorods in the NIR area due to the deeper penetration of evanescent waves, a higher surface-volume ratio, better crystallinity, more adhesive interactions with salt molecules, larger surface roughness and higher-order dispersion compared to the other coated ZnO nanostructures. © 2020 The Royal Society of Chemistry.