The contamination of aquatic sediments by metals is a worldwide phenomenon and its assessment is a fairly complex issue, as numerous factors affect the distribution of particular contaminants in the environment, as well as their bioavailability. Wigry Lake, as the object of this study, is almost a perfect water body for such considerations. It has been well investigated and densely sampled (up to 459 sediment samples). The quantities of seven metals were determined using the atomic absorption spectrometry (AAS) or inductively coupled plasma (ICP)-MS methods, following previous extraction in a microwave oven. The levels of concentration of the examined elements were as follows (min–max (mg·kg−1)): Cd—0.003–3.060; Cr—0.20–22.61; Cu—0.02–59.70; Fe—80–32,857; Mn—18–1698; Pb—7.0–107.5; Zn—3.1–632.1. Significant differences were also registered in terms of particular metal concentrations in different sediment types found at the lake bottom. Five different geochemical backgrounds and sediment quality guidelines implemented in the study enabled a very scrupulous contamination assessment of the lake sediments’ condition, as well as the evaluation of the natural and anthropogenic contribution to the enrichment of examined sediments in metals. Although Wigry Lake is situated in a pristine region, it is still subject to anthropopressure, which seems to be the lowest in respect to Cr and Mn, while the highest in the case of Pb. The chemoecological state of the lake was ultimately assessed as good. The study highlighted the necessity of an integrated approach to the assessment of contamination or pollution in the course of an environmental research.