This paper presents the results of recharge estimation and water table variation analyses of the Coastal Aquifer System, located in the Rio Grande do Sul Coastal Plain (Brazil). Water level data from 11 wells was processed and analyzed from May 2014 to Apr 2020, applying autocorrelation and cross-correlation methods to evaluate the aquifer memory effect and mean response time to rainfall events, respectively. The seasonality of the response time was observed through splitting the data series in windows of 90 days, overlapped by 45 days. Recharge rates were obtained with the Water Table Fluctuation (WTF) daily applications (RISE and MRC), considering specific yields of 20%, 25% and 30%. Water level data smoothing with moving averages and time series filters were necessary, to remove level rises not associated with precipitation events within the aquifer average response time, The autocorrelation and cross-correlation displayed fast, intermediate, and slow responses for the wells, with median response times for the time windows from 0 and 1 days (wells in aquifer layers of fine to medium sands) to 10 days (wells in aquifer layers of higher clay content). The recharge rates of 0,74 to 2,42 mm/day and Recharge/Precipitation ratios from 19–46% were obtained (Sy = 25%, mean between RISE and MRC results). The study presents the importance of level data processing and filtering to daily WTF applications and displays the differences in the behavior of the wells in the Coastal Aquifer System.