Spatial synchrony occurs when geographically separated time series exhibit correlated temporal variability. Studies of synchrony between different environmental variables within marine ecosystems worldwide have highlighted the extent of system responses to exogenous large-scale forcing. However, these spatial connections remain largely unstudied in marine systems, particularly complex coastlines, where a paucity of field observations precludes the analysis of time series. Here, we used time-frequency analyses based on wavelet and wavelet coherence (WC) analysis to quantify the synchrony (co-variations) between environmental time series derived from MODIS (moderate resolution imaging spectroradiometer) in the topographically complex inner sea of Chiloé (ISC, 41–44°S) for the 2003–2022 period. We find that the strength of the synchrony between chlorophyll a (𝐶ℎ𝑙𝑎) and turbid river plumes (for which we use remote sensing reflectance at 645 nm, 𝑅𝑟𝑠645) varies between the northern and southern areas of the ISC; higher synchrony, measured as the WC between these variables, is observed along the northern basin where water and particle exchanges with the Pacific Ocean are reduced. The WC analysis showed higher synchrony between these variables, with dominant periodicities of 0.5 and 1 year resulting from the hydrological regime of the freshwater input in the area that persisted throughout the 2004–2018 period. Our results suggest that the strong and significant spatial synchrony at the regional scale is likely related to the phases of large-scale climatic oscillations, as inferred through the partial wavelet coherence analysis. Potential mechanisms driving spatial synchrony are discussed in the context of climate and oceanographic regimes in the area.