Abstract To examine limnological conditions in Lake Ogawara on the Pacific coast of northwestern Japan, we investigated the magnetic properties of dredged bottom sediment originally collected from the lake in the summer of 2011. We used non-destructive methods to measure the low-field magnetic susceptibility shortly after sampling, and anhysteretic remanent magnetization (ARM) was assessed in 2012 and 2015. The ARM acquisition and demagnetization curves from littoral sites showed several patterns that reflect the provenance of the sediments. At water depths below 10 m, the magnetic susceptibility and ARM of greenish black mud with high organic content decreased considerably with the increase in water depth, but ARM increased slightly at water depths greater than 16 m. We also found that the magnetic concentrations of mud samples were reduced markedly during a period of storage for about 3 years. We attributed these reductions to diagenetic loss of magnetic minerals, which had been enhanced at deeper sites. It is possible that the ARM carriers in deeper areas were derived from authigenic formation of iron sulfide or from deposition of suspended matter in the hypolimnion water. We propose that the magnetic properties of surficial sediments are controlled by limnological stratification of the brackish lake water, thus possibly providing an analog for down-core variations of magnetic parameters associated with the modification of magnetic minerals during reductive diagenesis.