Bone Bay, a semi-enclosed marine region within the Coral Triangle, holds significant potential for fisheries. Understanding oceanographic parameters, particularly sea surface temperature (SST) and chlorophyll-a (Chl-a), is crucial for sustainable fisheries management. This study investigated the influence of ENSO and the Indian Ocean Dipole (IOD) on SST and Chl-a variability in Bone Bay using Niño3.4 and Dipole Mode Index (DMI) data from NOAA (2010–2020). SST and Chl-a were analyzed through remote sensing techniques using Aqua-MODIS satellite imagery and spatial-temporal methods. Additionally, statistical analysis was conducted using the relationship analysis with cross-correlation method to evaluate the relationship between ENSO, IOD, and oceanographic parameters. The results indicated that extreme ENSO and IOD events, particularly in 2015–2016, do not exhibit a strong correlation with Chl-a variability. The Chl-a anomaly correlation values was 0.03 for ENSO and was 0.09 for IOD. Similarly, SST anomalies show a weak correlation with ENSO at 0.04 and a correlation with IOD at 0.24. The semi-enclosed nature of Bone Bay likely buffers it from large-scale climatic events, with local hydrodynamic factors playing a more dominant role. These findings provide critical insights for fisheries resource management in semi-enclosed waters and emphasize the need for localized oceanographic studies to inform policy decisions.