With the increasing seriousness of groundwater(or geothermal groundwater)  pollution,the need for modeling and predicting groundwater flow and solute mass(or contaminants) transport in groundwater system of the basement rock aquifers under the condition of nature and human activity  has imposed extraordinary demands on the field of groundwater modeling, which has been brought to the great notice of experts at home and abroad.  In accordance with the geological and hydrogeologic conditions of Kunming city geothermal field,which is a large low temperature geothermal groundwater field, a quasi-three dimensional numerical model with temperature and pressure variation in the geothermal leaky aquifers system is presented based on the authors' recent years' research in this paper. It is coupled with the well-known groundwater flow model and a heat transfer model and a mass(contaminant) transport model. The above model is applied to describe the geothermal groundwater hydraulic-level and concentration of the simulated mass factor(contaminant)  versus time of Z₂dn aquifer in II block under the situation of exploitation.The simulated results agree well with the observed facts.The average error of geothermal water hydraulic-level is less than 1.5 meter,and the average error of chlorin ion and vitriol ion are both less than 3 to 5 percent. It is revealed that the present model is reliable and practical. Finally, the changes of the geothermal water seepage field and the mass(contaminant) concentration is evaluated and predicted quantitatively under the current scale of exploitation. The appropriate corresponding counter-measures to sustainable exploitation and utilization have been proposed.