Lake Junttiselka, located in central Finland, has been loaded by effluents from Pyhasalmi Zn–Cu mine since 1962 and also receives Pyhasalmi municipal effluent. A total of 32 top sediment samples (0–2, 2–4, and 4–6 cm) were collected in October 2005 and March 2006 to examine the seasonal variation in sediment composition. Furthermore, two sediment cores of 1 m were taken from the northern and southern parts of the lake (Junttiselka_N, Junttiselka_S) to investigate the sedimentation history. Electrical conductivity (EC) was measured from the sediment in situ, and sediment pH, redox values, and EC were measured in the winter from the top samples. The sediment samples were freeze-dried and multi-element determinations were performed using ICP-MS on nitric acid extracts (EPA 3051, acid soluble fraction, AF) and on ammonium acetate extracts (bioavailable fraction, BF). The composition of crystalline and semi-crystalline fractions (CF) was calculated by the formula CCF = CAF – CBF. Due to the high clay content of till in the catchment area, the Al, K, and Mg concentrations in the natural lake sediments (>49 cm) are greater than the average level in lake sediments of Finland (AF). Soil cultivation has increased the sedimentation of fines, which has further increased Al, K, and Mg concentrations in the lake sediments (49–19 cm). Mine effluents have had the greatest impact on sediment concentrations of Cu and Zn, with the recorded levels of 166 mg/kg and 434 mg/kg (<19 cm), respectively, being nine- and threefold greater than the natural concentration level. Also, Ca and S concentrations are elevated. The electric conductivity of pore water was elevated at a depth of 1 m. Seasonal variation in the composition of Junttiselka top sediments is linked to the oxic/anoxic conditions in the water column during the autumn to winter period. The greatest variation was recorded in the 0–2 cm layer in Junttiselka_S, where CaBF and SBF concentrations were three and sixfold higher in the winter than in the autumn. MgBF, PbBF, SrBF, CrBF, PBF, UAF, and SeAF concentrations also increased in the winter, but MnBF, CuBF, CdBF, CoBF, ZnBF, BaBF, NiBF, FeBF, and AlBF decreased. The seasonal variation in composition was less for CF than for BF, and was also partially different. The most significant difference was an increase in CaCF and SCF concentrations in the winter in Junttiselka_S, with the reverse situation being observed in Junttiselka_N. Furthermore, the FeCF concentration increased in Junttiselka_N. Equimolar variations in Ca and S suggest that the precipitation and dissolution of gypsum is the most notable seasonal process in the top sediment layer. The seasonally precipitated S corresponds to only 1.4% of the total load of S from the mine effluents.