Chemical analysis was performed on sediment core samples collected from three salt lakes, Amara Lake, Caineni Lake, and Movila Miresii Lake, located in the northeast of the Romanian Plain. The concentration of 10 main elements, 6 heavy metals (HMs), 8 rare earth elements (REEs), and 10 trace elements (TEs)—determined using neutron activation analysis (NAA)—showed variability dependent on the depth sections, lake genesis and geochemical characteristics (oxbow, fluvial harbor/liman and loess saucer type). The assessment of pollution indices (contamination factor, pollution load index, geoaccumulation index, and enrichment factor) highlighted low and moderate degrees of contamination for most of the investigated elements. Principal component analysis (PCA) extracted three principal components, explaining 70.33% (Amara Lake), 79.92% (Caineni Lake), and 71.42% (Movila Miresii Lake) of the observed variability. The principal components extracted were assigned to pedological contribution (37.42%—Amara Lake, 55.88%—Caineni Lake, and 15.31%—Movila Miresii Lake), salts depositions (due to the lack of a constant supply of freshwater and through evaporation during dry periods), atmospheric deposition (19.19%—Amara Lake, 13.80%—Caineni Lake, and 10.80%—Movila Miresii Lake), leaching from soil surface/denudation, rock weathering, and mixed anthropogenic input (e.g., agricultural runoff, wastewater discharges) (13.72%—Amara Lake, 10.24%—Caineni Lake, and 45.31%—Movila Miresii Lake).