Nuclear reactor process control is typically monitored for pure β-emitting radionuclides via manual sampling followed by laboratory analysis, leading to delays in data availability and response times. The development of an in situ microfluidic Lab on Chip (LoC) system with integrated detection capable of measuring pure β-emitting radionuclides presents a promising solution, enabling a reduction in occupational exposure and cost of monitoring whilst providing improved temporal resolution through near real-time data acquisition. However, testing prototypes with radioactive sources is time-consuming, requires specialist facilities/equipment, generates contaminated waste, and cannot rapidly evaluate a wide range of designs or configurations. Despite this, modelling multiple design parameters and testing their impact on detection with non-radioactive substitutes has yet to be adopted as best practice. The measurement of pure β emitters in aqueous media relies on the efficient transport of photons generated by the Cherenkov effect or liquid scintillators to the detector. Here we explore the role of numerical modelling to assess the impact of optical cell geometry and design on photon transmission and detection through the microfluidic system, facilitating improved designs to realise better efficiency of integrated detectors and overall platform design. Our results demonstrate that theoretical modelling and an experimental evaluation using non-radiogenic chemiluminescence are viable for system testing design parameters and their impact on photon transport. These approaches enable reduced material consumption and requirement for specialist facilities for handling radioactive materials during the prototyping process. This method establishes proof of concept and the first step towards numerical modelling approaches for the design optimisation of microfluidic LoC systems with integrated detectors for the measurement of pure β emitting radionuclides via scintillation-based detection.