Simple Ocean Data Assimilation reanalysis and other data were used to explore seasonal variation characteristics of freshwater transport between the Arabian Sea (AS) and the Equatorial Western Indian Ocean (EWIO), and the Gulf of Oman (GOO). Freshwater budget in the AS is characterized by a basic balance and its seasonal variation is also present. Our results indicate that the amount of input freshwater from the EWIO and river discharge is roughly equal to the amount of freshwater output to GOO and lost caused by the evaporation overwhelming the precipitation (P–E). The lost freshwater via air-sea exchange (i.e. P–E) is compensated by freshwater flux from the EWIO and the Bay of Bengal (BOB), which plays a key role in maintaining the basic balance of salinity over the AS. Net freshwater flux in the AS is negative (i.e. lost freshwater) from January to June together with December, and positive (i.e. receive freshwater) during July and November with a maximum positive value in September. The seasonal variation characteristics of net freshwater flux in the AS shows a single remarkable peak. Along the 9°N section, freshwater exchange between the EWIO and the AS primarily occurs from the surface to 200 m depth, with a multi-year averaged net flux into the AS of about 0.1×10⁶ m³/s. From October to next March, the BOB low-salinity water extends into the AS at above 60 m depth through the southwest of the Indian peninsula. In summer and autumn, the transport associated with the Great Whirl located at the east of Somali Peninsula, is characterized by low (high) salinity water in the west (east) of the whirl transported northward (southward) into the AS (equatorial Indian Ocean). This transport during these two seasons is largest in a year with its influence can extend downward to about 300 m depth, which forms in June, then peaks in August and September, and finally decays rapidly in November. Water exchange between the AS and the GOO is relatively weak, and has a sandwich-like three-layer structure in vertical direction: high salinity water intrudes from GOO into the AS in the upper 10 m layer and in the bottom layer between 175 m and 400 m depth; whereas in the middle layer (i.e. 15 m to 170 m depth) low salinity water is transported from the AS to the GOO. On multi-year average, a net freshwater transport of about 0.39×10⁴ m³/s is further estimated into the GOO from the AS across the section along the GOO mouth.