Sea level rise is an important and topical issue in the South Pacific region and needs an urgent assessment of trends for informed decision making. This paper presents mean sea level trend assessment using harmonic analysis and a hybrid deep learning (DL) model based on the Complete Ensemble Empirical Mode Decomposition with Adaptive Noise (CEEMDAN) technique, Convolutional Neural Network (CNN), Gated Recurrent Unit (GRU) and Neighbourhood Component Analysis (NCA) to build a highly accurate sea level forecasting model for three small islands (Fiji, Marshall Island and Papua New Guinea (PNG)) in the South Pacific. For a 20-year period, the estimated mean sea level rise per year from the harmonic computation is obtained: 112 mm for PNG, 98 mm for Marshall Island and 52 mm for Fiji. The DL procedure uses climate and environment-based remote sensing satellite (MODIS, GLDAS-2.0, MODIS TERRA, MERRA-2) predictor variables with tide gauge base mean sea level (MSL) data for model training and development for forecasting. The developed CEEMDAN-CNN-GRU as the objective model is benchmarked by comparison to the hybrid model without data decomposition, CNN-GRU and standalone models, Decision Trees (DT) and Support Vector Regression (SVR). All model performances are evaluated using reliable statistical metrics. The CEEMDAN-CNN-GRU shows superior accuracy when compared with other standalone and hybrid models. It shows an accuracy of >96% for correlation coefficient and an error of <1% for all study sites.