This article contains analytical data on the spatial and temporal variability of physical-chemical indicators of water quality in the Cunas River, collected in areas of seven localities, during the rainy and dry period from 2014–2016. The physical-chemical parameters determined in situ were carried out with Hanna Instruments' portable equipment (conductivity, dissolved oxygen, total dissolved solids, temperature, pH and turbidity). Water samples were also collected at a depth of 20 cm in two-liter plastic bottles for the analysis of nitrate, phosphorus, BOD5 and heavy metals. The determination of nitrate and phosphorus was performed with the MD 600/MaxiDirect photometer and BOD5 by the respirometric method. The determination of heavy metals was performed by atomic absorption spectrometry using a Shimadzu brand AA-6800 atomic absorption spectrophotometer. The development of this data set can serve as a basis for establishing a monitoring program to conserve the aquatic environment and ensure its various water uses.