This paper intends to show how the radio frequency-electromagnetic (RF-EM) method can be successfully used in coastal wetlands, onshore and in shallow water. It characterizes and reveals geological and hydrogeological singularities that are often hidden by recent sediments and allows target sampling and consequent detection of ecological particularities. RF-EM methods have traditionally been used to detect the presence of groundwater or the existence of subsurface contamination plumes. The great majority of such studies have been conducted on land and to a lesser extent on freshwater lakes but rarely in coastal waters. Previous research in Portugal has shown that despite the attenuation effect of salt water, very valuable information can be obtained with the use of electromagnetic methods, wherever resistivity contrasts exist. In the current case study, RF-EM surveys were carried out in the Estuary of the Guadiana River, in order to understand the importance of geological structures on the formation of the wetland and the influence of groundwater discharge on the existing ecosystem. Structures detected on land were also identified in the tidal channels. Freshwater fault springs were localized; their biota is characterized and the nutrients analysed. The results showed a clear increase in nitrate and silica concentration near the submarine springs, with impact on the planktonic communities, which is most evident in chlorophyll a. This is especially relevant during the end of summer and autumn when a potential limitation of these nutrients exists that can increase the occurrence of toxic blooms in the salt marshes and lower estuary. Copyright © 2012 John Wiley & Sons, Ltd.