High frequency monitoring in environmental studies is increasingly being used due to the availability of equipment and quick response. With high frequency time series, it is possible to extract short-term responses during and after a rain event, which is not captured by conventional monitoring. The aim of this study is to evaluate the superficial water quality change of a stream in a preserved area in Atlantic Forest by short-term data (hour interval). The Cubatao do Sul watershed is located in the Central Coast region of the state of Santa Catarina in Brazil. Rain height and water quality parameters were monitored using rain gauge and multiparameter probes. Two fluviometric sections were also monitored - one in Vargem do Braco stream (FS1), which is mainly native forest (dense ombrophilous forest), and the other in Cubatao do Sul River (FS2), which is influenced by urban, agricultural and sand extraction uses. The temperature and nitrate ion permanency curve in FS1 showed slightly lower values during rainy events, but an opposite behavior was observed for turbidity. On the other hand, the permanency curves during rainy periods of FS2 presented lower conductivity and ammonium ion. When the dry and rainy periods were statistically compared, there was a significant difference for temperature, conductivity, pH, nitrate ion, turbidity and dissolved oxygen for FS1, and temperature, conductivity and turbidity for FS2. The water quality of the Cubatao do Sul watershed is influenced by stream flow and has a short-term time response considering the rain events. The oscillation of the monitored parameters between two periods, dry and rainy, is smaller in native forest than urban and rural land use.