The geochemistry and vertical stratification of shallow meltwater ponds at 78°S near Bratina Island (McMurdo Ice Shelf) have been determined for late winter (October) and summer (January) conditions as part of the Latitudinal Gradient Project. Of the five frozen ponds investigated in October, all were stratified with respect to conductivity, and three had highly saline basal brines beneath the ice at temperatures of −16 to −20°C. In the ice column, inclusions of saline fluid were observed in channels between ice crystals; the abundance increasing with depth and decreasing ice crystal size. In January, seven of the ten ponds investigated (including ponds sampled in October) retained conductivity stratification, whereas significant thermal stratification was observed in only three ponds (maximum ΔT = 5.5°C). Basal brines, ice and meltwaters were Na-Cl or Na-SO4 dominated. FREZCHEM52 modelling, supported by changes in ion ratios, indicated that the precipitation of mirabilite (Na2SO4.10H2O) and gypsum (CaSO4.2H2O) during progressive freezing is an important determinant in chemical evolution of the basal brine. High pH (8.8–11.2) and over-saturation with respect to dissolved oxygen (> 20 mg L−1) in summer, and the presence of sulphide ions in basal brines in winter, occurred in those ponds which experienced high biological productivity during the summer months.