The northern shallow seas of Australia exhibit significant interannual mass variation characteristics. The sources and physical mechanisms underlying these variations are not fully understood and warrant further investigation. To this end, we utilized satellite gravity, satellite altimetry, and Global Navigation Satellite System (GNSS) to study and analyze sea level changes and their loading effects in this region from 2003 to 2022. The results indicate that sea levels in the northwestern sea and the Gulf of Carpentaria (GOC) have been continuously rising, primarily due to the increase in ocean water mass (0.37±0.05 cm/a and 0.43±0.07 cm/a, respectively). The contribution of oceanbottom deformation caused by mass changes to sea level rise accounted for 4% and 5%, respectively. However, using reanalysis products to study the steric sea level results in significant errors, leading to an underestimation of the annual amplitude by 63%. Monsoons and monsoon rainfall drive the increase in water mass in GOC, while ocean currents outside the GOC also significantly influence the mass changes, with an annual total outflow flux of 72.09 Gt. We also found that a single GNSS station on island within the GOC can effectively capture the seasonal and interannual water mass variations in GOC. For seasonal changes, the correlation between vertical displacement and gulf mass variation reached 0.90, and the station was able to recover 72.7% of the interannual amplitude of long-term ocean mass changes in the GOC.