The Bathonian age Inverbrora Member of the Brora Coal Formation, northern Scotland, was deposited in a predominantly fresh- water coastal lagoon setting. However, two prominent shell beds within the mostly argillaceous succession have been interpreted as resulting from temporary inundation of marine water and establishment of brackish conditions. The ensuing lagoon hydrology and paleoenvironment were investigated by measuring stable isotopic (δ18O and δ13C) and trace element (Mg, Sr, Mn, Ba) variations within five exceptionally well preserved aragonite shells of the bivalve Isognomonmurchisoni. Transects were sampled across the visible growth banding with a resolution of 0.25−0.15 mm for stable isotopes, and 0.05 mm for trace elements. Oxygen and carbon isotope data define a broadly covariant trend (δ18O between +0.4‰ and −4.8‰ Peedee belemnite [PDB]; δ13C between +2.2‰ and −0.7‰ PDB) that supports a variably brackish-water setting with slight seasonal evaporation. Absolute trace element values vary from shell to shell but show consistent patterns of covariation. Profiles of Mg/Ca across shell layers display multiple sharp, episodic minima that are coincident with peaks in Sr/Ca and Ba/Ca. This is interpreted as documenting inundation of the restricted, brackish-water lagoon by relatively cooler seawater, leading to a temporary increase in metabolic activity of the bivalves. Less frequent minima in Mg/Ca, Sr/Ca, δ18O, and δ13C record fresh-water influx and dramatic salinity reduction in the lagoon. Bivalve metabolic efficiency was decreased, and in some cases breaks in shell growth occurred. This study shows that in hydrodynamically complex settings, trace element variation in bivalve shells can provide a detailed record of short-term environmental change.