Despite the known influence of groundwater conditions and nitrogen application on crop growth and the soil microenvironment, less information is available on the influence of groundwater depth and nitrogen application amount on the movement and accumulation of soil water and residual nitrate in deep soil in summer maize–winter wheat rotation systems. Therefore, a large lysimeter experiment was conducted to examine how groundwater depth and nitrogen application amount influence the transport and accumulation of soil water and nitrate in the summer maize (Zea mays L.)–winter wheat (Triticum aestivum L.) rotation system. The results showed that nitrogen reduction increased soil water storage both in the summer maize and winter wheat fields. The residual soil nitrate accumulation in the entire soil profile of summer maize and winter wheat under deeper groundwater depth treatment was higher than that of shallow groundwater depth treatment. Hence, the deeper the groundwater depth, the longer the nitrate transport path, and the nitrate that would have entered the groundwater accumulates in deep soil. The residual soil nitrate accumulation in the whole soil profile of winter wheat was 76.05–130.11 kg ha−1 higher than that of summer maize. Structural equation models (SEMs) showed that the nitrogen application amount not only exhibited a directly positive effect on the residual soil nitrate accumulation but also indirectly influenced it by regulating total soil nitrogen; groundwater depth only exhibited a directly negative effect on residual soil nitrate accumulation; and soil depth had an indirect positive effect on residual soil nitrate accumulation through the regulation of soil water storage. Together, our findings prove that groundwater depth and nitrogen application amount jointly regulate the residual soil nitrate accumulation in agricultural soil rotated with winter wheat and summer maize. Therefore, in formulating a fertilization strategy for regional agricultural green development, it is necessary to consider the fertilizer application amount rate and the groundwater depth.

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