The extensive eastern boundary of Everglades National Park (ENP) in south Florida (USA) is subject to one of the most expensive and ambitious environmental restoration projects in history. Understanding and predicting the water quality interactions between the shallow aquifer and surface water is a key component in meeting current environmental regulations and fine-tuning ENP wetland restoration while still maintaining flood protection for the adjacent developed areas. Dynamic factor analysis (DFA), a recent technique for the study of multivariate non-stationary time-series, was applied to study fluctuations in groundwater quality in the area. More than two years of hydrological and water quality time series (rainfall; water table depth; and soil, ground and surface water concentrations of N-NO3-, N-NH4+, P-PO4(3-), Total P, F-and Cl-) from a small agricultural watershed adjacent to the ENP were selected for the study. The unexplained variability required for determining the concentration of each chemical in the 16 wells was greatly reduced by including in the analysis some of the observed time series as explanatory variables (rainfall, water table depth, and soil and canal water chemical concentration). DFA results showed that groundwater concentration of three of the agrochemical species studied (N-NO3-, P-PO4(3-)and Total P) were affected by the same explanatory variables (water table depth, enriched topsoil, and occurrence of a leaching rainfall event, in order of decreasing relative importance). This indicates that leaching by rainfall is the main mechanism explaining concentration peaks in groundwater. In the case of N-NH4+, in addition to leaching, groundwater concentration is governed by lateral exchange with canals. F-and Cl- are mainly affected by periods of dilution by rainfall recharge, and by exchange with the canals. The unstructured nature of the common trends found suggests that these are related to the complex spatially and temporally varying land use patterns in the watershed. The results indicate that peak concentrations of agrochemicals in groundwater could be reduced by improving fertilization practices (by splitting and modifying timing of applications) and by operating the regional canal system to maintain the water table low, especially during the rainy periods.