Rising nitrate contamination in water systems poses significant risks to public health and ecosystem stability, necessitating advanced modeling to understand nitrate dynamics more accurately. This study applies the long short-term memory (LSTM) modeling to investigate the hydrologic and environmental factors influencing nitrate concentration dynamics in rivers and aquifers across the state of Alabama in the southeast of the United States. By integrating dynamic data such as streamflow and groundwater levels with static catchment attributes, the machine learning model identifies primary drivers of nitrate fluctuations, offering detailed insights into the complex interactions affecting multi-year nitrate concentrations in natural aquatic systems. In addition, a novel LSTM-based approach utilizes synthetic surface water nitrate data to predict groundwater nitrate levels, helping to address monitoring gaps in aquifers connected to these rivers. This method reveals potential correlations between surface water and groundwater nitrate dynamics, which is particularly meaningful given the lack of water quality observations in many aquifers. Field applications further show that, while the LSTM model effectively captures seasonal trends, limitations in representing extreme nitrate events suggest areas for further refinement. These findings contribute to data-driven water quality management, enhancing understanding of nitrate behavior in interconnected water systems.