The dataset compiles in situ observational data obtained during the R/V Mirai MR16-09 cruise (2017-01-21 to 2017-02-03) off western Patagonia, Chile. In terms of chemical variables, the dataset includes information of nutrients, nutrient ratios, dissolved oxygen and ammonium concentrations. Water samples for nutrients analysis were collected in duplicate at discrete sampling depths (0, 10, 25, 50 and 100 m depth) from a 36-Niskin bottles (12-liter each) SBE carousel water sampler. The samples were taken into 10 mL polyacrylates vials which were rinsed three times before filling. The closed vials were put into a water bath, set at ambient temperature (22 ± 1°C), for about 30 minutes to stabilize the temperature of the samples, after which were analyzed in an auto-sampler tray within 24 hours after collection. Nitrate, phosphate, silicate and ammonium concentrations were determined using the QuAAtro 2-HR systems (BL-Tech), which the detection limits were 0.02 μmol kg⁻¹, 0.003 μmol kg⁻¹, 0.03 μmol kg⁻¹, and 0.02 μmol kg⁻¹, respectively.