The Ganges Submarine Delta is a key land-sea transitional area in the northeastern Indian Ocean. An understanding of sediment distribution, provenance, and transportation in this area is of great importance for understanding its sedimentary environment and the sediment “source-sink” system of the northeastern Indian Ocean. This study aimed to identify the provenances and transport patterns of fine-grained sediments in the Ganges Submarine Delta through analysis of the grain size and clay mineral content of 84 surface sediment samples. Sediment illite, chlorite, kaolinite, and smectite contents were ∼66%, 18%, 11%, and 5%, respectively. Sediment illite content decreased from north to south; smectite and chlorite decreased and increased from northwest to southeast, respectively; kaolinite content was highest in the south. Spatial cluster analysis of the four clay minerals grouped the study area into two provinces: province I in the north is characterized by a clay mineral assemblage similar to that of the Ganges-Brahmaputra rivers; province II in the south is characterized by deep water and changes to clay mineral characteristics due to the mixing of material originating from the Indian Peninsula. This study used the illite/(smectite + chlorite + kaolinite) and kaolinite/illite ratios to discuss sediment transport paths in the two provinces. Himalayan material is widely distributed throughout the study area, and mainly transported from the estuary to the southwestern area by the tides, plume, and monsoons; sediments of the Mahanadi river are transported from southwest to northeast by the southwest monsoon, thereby affecting the sediment composition of province II.