This work explores the effects of embedded software-driven measurements on a sensory target when using a LED as a photodetector. Water turbidity is used as the sensory target in this study to explore these effects using a practical and important water quality parameter. Impacts on turbidity measurements are examined by adopting the Paired Emitter Detector Diode (PEDD) capacitive discharge technique and comparing common embedded software/firmware implementations. The findings show that the chosen software method can (a) affect the detection performance by up to 67%, (b) result in a variable sampling frequency/period, and (c) lead to an disagreement of the photo capacitance by up to 23%. Optimized code is offered to correct for these issues and its effectiveness is shown through comparative analyses, with the disagreement reduced significantly from 23% to 0.18%. Overall, this work demonstrates that the embedded software is a key and critical factor for PEDD capacitive discharge measurements and must be considered carefully for future measurements in sensor related studies.