The Odiel River (Huelva, southwest Spain) carries acidic water originating from mine waste contamination, including massive sulphide ore deposits. As the river approaches the coastal estuary, tidal factors influence both sediment and water dynamics. As water velocity decreases, sediment load transport capacity also decreases, building river bars consisting of boulders upstream and sands downstream. Salt water near the estuary affects river water chemistry by neutralizing acidity derived from mine wastes. The occurrence of pyrite mud and hydrated iron sulphate efflorescence, precipitated from acidic waters, is plugged by marine water with chloride, which precipitates from the salt water. Hymap airborne hyperspectral data were used to evaluate tidal influence using spectral features. Grain size variations on river pebble bars, localized crusts of variably hydrated iron sulphate and oxides and cation exchange with chloride salts in the lower river segment as it enters the estuary were spectrally described and mapped. The presence of vegetation proved particularly problematic for the spectral identification of contamination products as well as the precise delineation of inundated areas along the river. The transition from dry to wet zones is the crucial challenge in using spectral imagery to identify and track contaminants in the river and along its flood plain. The use of a reference mineralogical spectral library, developed in the laboratory, requires a careful geological context evaluation to provide efficient environmental information on contamination parameters. Based on hyperspectral analyses of critical spectral features, river locations that may be a key for tracing significant, future contaminant fluctuations were identified.