Methods for real-time in situ analysis are needed for the monitoring and detection of pollutants and nutrients in water bodies. In situ instruments reduce the analysis time and decrease the chance of contamination or altering of the sample if taken to the laboratory. For this purpose, a mobile total analysis system is being developed for real-time environmental monitoring. The sensing platform, based on either an autonomous underwater vehicle or remotely operated vehicle, consists of an integrated flow-through channel with a chemically sensitive strip on one side of the channel and an optoelectronic detector opposite the strip. The strip contains an analyte-specific reagent that changes colour upon reaction with the analyte of interest introduced through the flow channel. In determining the feasibility of the design, the detection of copper ions was used as the case study. The interpretation strategy, referencing and calibration from the lab experiments including the effects of flow are shown.