Land reclamation not only provides valuable space for urban development, but also creates an upper aquifer in fill materials. Analysis of groundwater level (GWL) fluctuations in coastal aquifer formed due to land reclamation can provide important insight into the groundwater system (GWS) evolution, including the connectivity between the GWL and influencing variables (ocean tide and rainfall). This study presents wavelet analysis, multichannel SSA-wavelet analysis (MSSA-WA), and lag correlations to analyze the response of GWL to ocean tide and rainfall in the reclamation area of Zhoushan Island, China. The MSSA-WA results and the lag correlations show that the MSSA-WA provides better analysis results, specifically, clay layer and rainfall filtered information. The influence of the influencing variables on the upper GWL is relatively greater than the clay layer, and rainfall has a relatively stronger impact on GWLs than tides. The GWLs of the upper layer, SW18 and SW21, which are heavily influenced by influencing variables, can be predicted through variations in influencing variables. Finally, the analysis of the results shows that the lithology of different aquifers, offshore distance, preferential flow path, and pressure load can be factors between tides and GWLs. For rainfall and GWLs, different lithology of aquifers, properties of vadose zone, and topography can be influential factors. The combination method provides an optimization method for GWL fluctuations in coastal reclamation area with combined MSSA and wavelet analysis for correlation analysis between GWL and influencing variables (ocean tide and rainfall) and analysis of corresponding causes and influencing factors.