The monitoring of key parameters and analytes (including ions) in aquatic systems is crucial to our understanding of biogeochemical processes and their possible correlation with anthropogenic activities. The use of centralised analytical methodologies is most established for this purpose, but the risk of sample alteration during sampling and transport and the limited data acquisition frequency are promoting a paradigm shift towards in situ approaches. These focus on performing the measurement shipboard, from on site platforms or through submersible probes. This latter option is the most attractive for environmental scientists since it provides real-time profiles with high spatial and temporal resolution, even allowing the study of aquatic processes that evolve at the minute time scale. Potentiometric ion-selective electrodes, especially based on polymeric membranes, have therefore been widely used to detect important ions in marine and fresh water systems. Importantly, their inherent characteristics make them particularly suitable for implementation into submersible probes. This critical review highlights some recent examples related to the application of membrane electrodes for water analysis with particular attention to the efforts towards in situ detection. Sensor technology is sometimes overlooked in environmental analysis and this review aims to bring electrochemists, analysts and environmentalists together to better appreciate the strengths of membrane electrodes targeted to this aim.