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Groundwater heat pump (GWHP) systems are central heating and cooling systems that utilize groundwater heat. With the rapid development of this technology in China, it has become imperative to study the changes in the ground environment, including the flow features, heat transfer characteristics and clogging caused by long-term recharge, during the operation of GWHP systems. In this paper, a mathematical model considering the effect of particle deposition was proposed to describe a GWHP system based on the typical geological and hydrogeological conditions (i.e., a dual-structure strata) in Wuhan, China. During research on a GWHP engineering project in the Baibuting Garden community, four groundwater flow conditions (including no flow, forward flow, reverse flow and cross flow) and two typical flow modes (continuous and flushing modes) were considered. The groundwater temperature and flow rate were measured through measuring wells, and a comparison between theoretical and actual values shows that this model can provide an easy yet effective way to describe GWHP engineering. The seepage and temperature fields both display periodic trends under the continuous flow mode and can be significantly affected by well flushing. The central area is marginally influenced by groundwater flow when compared with the surrounding areas; for instance, the temperature fluctuation at MW3 can reach 8.2 °C, while the fluctuation reaches 2.9 °C at MW1. Particle deposition can affect the parameters of the ground environment; we find considerable correspondence between the concentration of deposited particles and the porosity. Moreover, both the concentration of deposited particles and the porosity change by a large margin after flushing, especially in regions around pumping wells (the concentration of deposited particles can fluctuate by 108 g/L, and the porosity can change by 0.055). [ABSTRACT FROM AUTHOR]