This paper discusses relationship among depositional environments, origin of the sedimentary organic matter and diatom fossil assemblage, combined with sequence stratigraphy in an incised-valley system. Interpretation of the environments and their changes was based on sedimentary facies, total sulfur (TS) content, and diatom assemblages. The quantity and composition of organic matter were estimated for the environmental interpretation on the basis of the total organic carbon (TOC) content, reflected-light fluorescent microscopy, and stable carbon isotope ratios of the organic matter (d 13 C org ). The Miocene to Pliocene Ishibane, Tatsunokuchi and Motohata formations in northeast Japan consist of estuarine and fluvial deposits that were formed during a rise and fall of sea level. The proportions of vitrinite and cutinite that are coarse-grained and terrestrial in origin are relatively high in fluvial deposits of the lowstand systems tract. The proportion of marine alginite, TOC content, and d 13 C org values increase upward in estuary deposits of the transgressive systems tract. This implies the increase in the influence of the sea and the estuarine bottom conditions becoming anoxic. The proportions of vitrinite and cutinite increase upward in the highstand systems tract, whereas the d 13 C org values and TOC content decrease upward. These reflect the strong influence of river discharge. Variations of diatom fossil assemblage of fresh water, brackish water, intertidal, coastal marine and open marine species indicate the same repetitions of transgression and regression in the Tatsunokuchi Formation. Therefore, the transgressive systems tract in the Tatsunokuchi Formation includes four cycles of transgression and regression, while highstand systems tract shows one cycle of transgression and regression.