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Over the last several decades, rising nitrate concentrations in springs discharging from north Florida's karstic Upper Floridan Aquifer have coincided with proliferation of algae in Florida spring runs and subsequent ecosystem degradation. As agriculture and development are primary contributors to groundwater nitrate and are predicted to continue expanding, understanding unique contributions and transmission pathways of nitrate pollution is vital to restoring impaired spring ecosystems. In this study, we use statistics and signal processing to analyze continuous nitrate timeseries data collected over five years at four north Florida springs. We quantified a significant, low-frequency annual signal in nitrate concentrations superimposed on increasing nitrate trends. We show nitrate concentrations at springs increase during the rainy season, potentially in response to recharge and seasonal fertilizer application. Thus, we suggest seasonal fluctuations observed in nitrate concentrations are caused by increased recharge of nutrient-rich soil waters through fractures that deliver water on relatively short timescales to conduits during the rainy season. We further speculate the steady, monotonically increasing concentration is maintained by accumulation of Nitrogen as slow flow through matrix porosity through the remainder of the year. Seasonal nitrate concentrations resulting from flow through karst aquifers may thus be poorly simulated using equivalent porous media models that are increasingly being used for nutrient management, because they do not capture heterogenous flow and transport dynamics.