The concentrations of five heavy metals (Cd, Cr, Cu, Pb, and Zn) in the sediments, water, phytoplankton, zooplankton, and macroalgae from Kongsfjorden Fjord and the freshwater lakes of Ny-Ålesund in the Svalbard archipelago were determined in order to describe the anthropogenic impacts related to the Ny-Ålesund town. Water samples from nine stations, sediment samples from 23 stations, plankton samples from five stations, and six species of macroalgae were collected and subjected to heavy metal analysis using atomic absorption spectrophotometry (AAS). Only Cu and Zn were detected in the water samples. The plankton samples had only Zn, Cu, and Cr. The average metal concentrations in macroalgae fell in the decreasing order of Cu > Zn > Cr > Cd > Pb. In sediment samples, the metal order was as follows: Zn > Cu > Cr > Pb > Cd. Multivariate statistical analyses including principal component analysis (PCA) and hierarchical cluster analysis (HCA) were used to identify the source of the metal contamination. The metals were found to originate from a blend of both anthropogenic and geogenic sources. Pollution monitoring indices including geoaccumulation index (Igeo), contamination factor, contamination degree (Cdeg), pollution load index (PLI), and potential ecological risk (PER) were calculated using the metal data. In the study area, Igeo values of the metals showed pollution grades from 0 (uncontaminated) to 6 (extremely contaminated). Cdeg fell in classes from 1 (low contamination) to 4 (very high contamination). PLI values ranged between 0 and 5.68. PER values expressed that except for a few stations located at higher elevations in the glacial outwash plains, all other sites were highly polluted. The high level of pollution indices in the sites can be attributed to the anthropogenic activities persistent in the study area.