Long-standing wastewater and reclaimed water irrigation systems degrade groundwater quality and thus pose great risks to local soils and even to human health. In this study, seasonal variations in hydrochemical characteristics of groundwater were assessed to determine possible processes that induce groundwater degradation. Beijing was used as the focus area. A total of 82 wells at the southeast irrigation region of Beijing were investigated in 2014. Descriptive statistics, correlation analysis, Piper diagram, and saturation indices were used to distinguish seasonal variations in hydrochemistry in shallow and deep groundwater and possible reclaimed water irrigation effects. The main natural controlling processes include mineral precipitation and dissolution, cation exchange reactions, and dilution effects in shallow and deep groundwater. However, cation exchange reactions are considered to be intense in deeper aquifer. Additionally, shallow groundwater sites subjected to salinization and nitrate contamination were associated with intensive agricultural input and reclaimed water leaching. Sites continuously contaminated by nitrate were mainly distributed on highly permeable sediments. Irrigation with deep groundwater may reduce soil drainage conditions due to a high percentage of sodium. Overall, seasonal replenishment for subterranean quaternary aquifers from rainfall or irrigation plays a vital role in seasonal variation in shallow groundwater hydrochemistry.