Currently, preclinical drug testing and disease modelling are based on static cell cultures and animal models that often fail at predicting the human pathophysiology. Alternatively, Organ-on-Chips (OoCs), dynamic microphysiological platforms, can be employed to recapitulate organ functions and mimic the cell's microphysiological environment. OoCs also promote the study of transport mechanisms and tissue barriers, such as the blood-brain barrier (BBB), a critical structure responsible for the regulation of the brain fluid microenvironment. Monitoring the ionic environment of the BBB and its variation due to the effect of drug testing is thus critical, indicating the need for integrated sensing elements. The rapid evolution of silicon technology and microelectronics has contributed to the development of field-effect transistors (FETs) for use as biosensors, ever since their first appearance in the 1970s. Such devices can provide real-time and label-free detection of target bioanalytes with high sensitivity. There are several types of FET-based biosensors based on different geometries and utilising various materials, but currently, no optimal consensus for a biocompatible FET-based biosensor with high sensitivity and reliability has been established. In the present thesis, floating gate FET-based sensors implementing flexible electrodes suspended on an optically transparent sensing area were designed and successfully fabricated for application on blood-brain barrier ion environment monitoring. Before the designing process, a thorough literature study on FET-based alternative solutions compatible with the BBB-on-chip application gave an overview of the available technology. It also indicated a lack of theoretical background behind the sensor's operation mechanisms. To face this issue, theoretical and simulation models were created based on the floating-gate MOSFET operation. Additionally, the electrical double layer (EDL) role, only included in models in the presence of a reference electrode is examined. The novelty of the sensor configuration lies with the implementation of an additional planar electrode in the sensing area of the OoC, tackling the issue of the external reference electrode use. Possible models describing the interaction between the additional electrode and the FGFET are created for comparison with experimental data. The novel sensor is designed aiming towards optimised sensitivity while also examining the effect of different configurations on the behaviour of the planar electrode. Dual-gate operation of the fabricated sensor in electrolyte indicates an increase of the output signal up to 16$\%$ compared to single-gate operation. In contrast to model predictions, the sensor does not operate in saturation mode, rendering the mathematical models ineffective. The simulation-based model is suggested for following applications after fine-tuning based on experimental data. Overall, a strong basis of the theoretical background was established, making ground for future studies.