The Low Carbon Development Strategy proposed in June 2009 by the government of Guyana in response to the Reducing Emissions from Deforestation and Forest Degradation in Developing Countries program has triggered evaluation of forest-related activities, thereby acting as a catalyst for improvements in Guyana’s small- to medium-scale gold mining industry. This has also shed light on areas committed to conservation, something that has also been handled by Non Governmental Organizations. This paper compares water quality and mercury concentrations in sediment from four main areas in Guyana, two that are heavily mined for gold using mercury amalgamation methods (Arakaka and Mahdia) and two that are considered conservation areas (Iwokrama and Konashen). Fifty-three sediment and soil mercury loadings ranged from 29 to 1,200 ng/g and averaged 215 ± 187 ng/g for all sites with similar averages in conservation and mining areas. Sediment loadings are within the range seen in French Guiana and Suriname, but conservation area samples had higher loadings than the corresponding uncontaminated baselines. Type of ore and location in the mining process seemed to influence mercury loadings. Mercury sediment loadings were slightly positively correlated with pH (correlation coefficient = 0.2; p value < 0.001) whereas no significant correlations were found with dissolved oxygen or turbidity.