Seasonal-varying internal tidal dynamics have a critical role in deep-water renewal in tropical shallow-silled fjords (e.g. Ambon Bay, Indonesia). Seasonal- and tidal-based longitudinal CTD casts from the slope of outer Ambon Bay (OAB) to the sill of Ambon Bay coupled with bottom-mounted current meters at the sill and in inner Ambon Bay (IAB, the fjord basin), were employed to investigate the internal tidal-sill slope interaction and the characteristics of deep-water inflow. Weaker stratification in the easterly monsoonal season than the transitional monsoonal season (dT/dz = ~0.02 °C/m cf. dT/dz = ~0.06 °C/m) drives the predominant sub-critical slope condition at the OAB slope causing more frequent tidal upwelling events in the easterly monsoonal season (13 events in a spring-neap sequence) than in the transitional monsoonal season (5 events). The magnitude of tidal upwelling in Ambon Bay, as measured by the depth from which water upwells, is stronger in the easterly monsoonal season (up to 200 m) than in the transitional monsoonal season (maximum: 115 m). The influx of upwelled water across the sill was controlled by the tidal excursion of the deep-water plume in the easterly monsoonal season and by the deep-water/sill density difference in the transitional monsoonal season. A series of deep-water renewal events in IAB within a spring-neap sequence (~2 weeks) in the easterly monsoonal season supplied a total inflow volume of 0.09 ± 0.02 km3 which can replenish approximately 80% volume of the IAB deep layer. This total inflow volume was smaller in the transitional monsoonal season (0.05 ± 0.01 km3), hence, only flushing 40% volume of the IAB deep layer. The knowledge of internal tidal waves and deep-water inflow in Ambon Bay presented here will be a key reference for future studies focused on water transport in Ambon Bay and other shallow-silled tropical fjords.