Germination paper (GP) is used as a growth substrate in plant development studies. Current studies bear two limitations: (1) The actual GP water content and variations in GP water content are neglected. (2) Existing irrigation methods either maintain the GP water content at fully sufficient or at a constant deficit. Variation of the intensity of water deficit over time for plants grown on GP is not directly achievable using these methods. In this contribution, a new measurement and control approach was presented. As a first step, a more precise measurement of water content was realized by employing the discharging process of capacitors to determine the electrical resistance of GP, which is related to the water content. A Kalman filter using an evapotranspiration model in combination with experimental data was used to refine the measurements, serving as the input for a model predictive controller (MPC). The MPC was used to improve the dynamics of the irrigation amount to more precisely achieve the required water content for regulated water uptake in plant studies. This is important in studies involving deficit irrigation. The novel method described was capable of increasing the accuracy of GP water content control. As a first step, the measurement system achieved an improved accuracy of 0.22 g/g. The application of a MPC for water content control based on the improved measurement results in an overall control accuracy was 0.09 g/g. This method offers a new approach, allowing the use of GP for studies with varying water content. This addressed the limitations of existing plant growth studies and allowed the prospection of dependencies between dynamic water deficit and plant development using GP as a growth substrate for research studies.