Soil CO2 and CH4 concentrations are crucial determinants of crop physiology and soil environment. This study aimed to investigate the dynamics of soil CO2 and CH4 concentrations and their correlations with soil nutrient content, enzymatic activities and root biomass at shallow groundwater levels. Lysimeter experiments were conducted at five groundwater depths (20, 40, 50, 60, and 80 cm) and three fertilizer application rates (low, 75%; normal, 100%; high, 125%). Soil CO2 and CH4 concentrations, physicochemical properties, and enzymatic activities were determined in the three growth stages of winter wheat crop, and plant biomass was measured post-harvest. Groundwater depth significantly (P ≤ 0.001) affected CO2 and CH4 concentrations and root parameters, and their critical values appeared at the groundwater depth of 50–60 cm. Soil water content presented quadratic function relation with CO2 concentration, and exhibited the linear correlation with CH4 concentration. As an aerobic respiration product, soil CO2 concentration showed significant positive correlations with organic matter and total N levels, urease, phosphatase and sucrase activities, and root biomass in winter wheat. Soil CH4 concentration depending on anaerobic microbial activity showed significant correlations with soil nutrients, such as soil organic matter, total N, and available K. Fertilization significantly impacted root parameters (P ≤ 0.001) and shoot biomass (P ≤ 0.05) instead of CO2 and CH4 concentrations. In contrast, groundwater depth emerged as a crucial factor as it affected soil physicochemical properties, soil enzymatic activities, root respiration, and winter wheat growth at shallow groundwater levels.