Heavy metals are difficult for bio-degradation and can produce severe damages to aquatic ecosystem and human society. Many previous studies of trace elements and heavy metals have been conducted in shallow lakes, but these studies usually considered one large lake as a homogeneous state, where the small-scale heterogeneous spatial patterns due to lake morphology or dominant macrophytes communities in the lake were usually ignored. Here, we conducted a detailed field survey in a large shallow Lake Liangzihu (divided into three sub-lakes) to investigate the spatial pattern of 12 trace elements and heavy metals in sediment, water and submerged plants. Our results indicated a low risk of heavy metal contamination in Lake Liangzihu based on the ecological risk index (< 100). However, As, Pb and Zn in sediment was evaluated as the moderate or stronger contamination in some sites according to the geoaccumulation index, and Ni in water was close to the safety levels of Chinese drinking water guidelines. Moreover, three metals (Ba and Sr in sediment and Ni in water) differed at the sub-lake level, and strong variation of most metals in sediment, water and submerged plants was found at the sampling site level, indicating an important role of small-scale spatial pattern. Concentrations of most of these elements in sediment were positively correlated, but not so for the elements in water, suggesting different processes for the dynamics of the trace element and heavy metals between the two media. There were also significant differences of the bioconcentration factor (BCF) among the four plant species. Vallisneria natans had strongest BCF for As, and Ceratophyllum demersum had the highest BCF for Ni. But the transfer factor between the sediment and the water did not differ among three sub-lakes. In summary, our study highlights the role of spatial heterogeneity in the distribution of trace elements and heavy metals in large shallow lakes, which should be considered in the safety assessment of heavy metals in shallow lakes.