This study investigates the temporal variability of mesoscale eddies in the Bay of Bengal (BoB) over a 29-year period (1993–2021) using satellite altimeters. High-resolution daily sea level anomaly data are considered to identify the mesoscale eddies in the BoB utilizing py-eddy-tracker, an automated eddy detection and tracking method. Wavelet coherence analysis was conducted to find a statistically significant relation between eddy properties and climate indices. The findings indicate that anti-cyclonic eddies are more susceptible to the consequence of the Indian Ocean Dipole (IOD) and El Niño Southern Oscillation (ENSO) than cyclonic eddies. Additionally, the joined impact of ENSO and IOD conceivably alters eddy activities across the BoB, as the second downwelling coastal Kelvin wave (dCKW) were absent. The mesoscale eddies exhibit correlations with climate indicators, suggesting that eddies get stronger during La Niña and negative IOD years and get weaker during El Niño and positive IOD years. This is because La Niña and negative IOD events intensify the second dCKW, while it weakens or becomes completely absent during El Niño and positive IOD years. Random Forest model was used to compare the influence of ENSO and IOD on the forecasting performance of the eddy properties. It was demonstrated that a unique positive IOD (+IOD) negatively affects the forecasting of eddy properties when using Sea Surface Temperature (SST) and SST anomalies. The findings bear importance in verifying and confirming the interactions between the ocean and climate.