The development and application of an analytical methodology for the pretreatment and determination of 253 multiclass pesticides, in lake sediment samples, using liquid chromatography coupled with mass spectrometry (LC-MS/MS) are described in this work. Sediments of lakes Volvi, Doirani, and Kerkini, located in northern Greece, were collected in two-time periods (fall/winter 2010 and spring/summer 2011) and analyzed, applying the developed analytical methodology. Microwave-assisted extraction (MAE) was applied to extract the pesticide residues from lake sediment samples. Analytical results were stored, categorized, and visualized using geographical information systems, in order to assess and observe spatial and temporal variations of the pollution. Main pesticides that were detected included the following: amitrole, tebuconazole, phoxim, diniconazole, sethoxydim, temephos, tetrachlorvinphos, pendimethalin, boscalid, disulfoton sulfone, lenacil, propiconazole, cycloxydim, pyridaben, and terbuthylazine. Amitrole, diniconazole, and tebuconazole were found to be common in all three lakes. Lakes Kerkini and Doirani exhibited increased concentrations during the first sampling period (winter 2010) with predominant pesticide classes, triazines/triazoles and organophosphates. Pollution is mainly located near the populated villages of the lakes and the nearby cultivations. During the second sampling period, pesticide concentrations appear lower and located in sediments near the center of the lake. Lake Volvi exhibits increased pesticide concentrations during the second sampling period, temporal and spatial variations and different pesticide profile pattern. Increased pollution occurs near the center of the lake during the first sampling period, mainly comprised by triazines/triazoles and organophosphates. During the second sampling period, the majority of the sediment samples demonstrated a different pesticide profile dominated by unclassified pesticides and triazines/triazoles. Mineralogical analysis of the samples demonstrates that sediments are mainly composed of clay, mud, and sand particles, and they present spatial variations. Near the center of the lakes, sediments appear to be more fine-grained with higher clay content and are more likely to adsorb pesticides.