Abstract Modern water quality gradients on the inner-shelf of the Great Barrier Reef (GBR) are influenced by catchment modification and increased terrigenous suspended sediment delivery. Proxy-based reconstructions of terrestrial sediment discharge are critical to trace the environmental drivers that modulate inshore water quality and to quantify the magnitude and timing of major changes. In this study we present high-resolution Porites coral rare earth element (REE) data over the period 1987–2012 from inshore Magnetic Island, GBR. Shale-normalized REE distributions in coral samples effectively captured the major features of seawater. Terrigenous sediment derived characteristics of shale-normalised REE and Y (e.g., higher ΣREE, reduced LREE depletion, and lower Y/Ho ratios) show linear relationships with each other on annual to multi-annual timescales thus providing a specific fingerprint for terrestrially derived turbidity. Temporal variation of the proxies generally shows spikes associated with increased water turbidity during strong summer floods. However, anomalous spikes coinciding with negligible river discharge during dry periods were also observed and highlight that data from non-flood year summers and winters show less predictable relationships possibly related to wind driven resuspension events, channel dredging and other as yet undetermined factors. Regardless, temporal variability of the proxies show synchronicity with tested environmental drivers (e.g., river discharge and rainfall) on multi-annual timescales with greater terrigenous influence during wet periods from the late-1980s to early-1990s, late-1990s to early 2000s and late 2000s to early-2010s, consistent with increased delivery of terrestrial sediment at those times. Cerium (Ce) anomalies showed complex behaviour during lower discharge seasons but have enhanced negative anomalies during strong flood-year summers when large flood plumes enriched in terrigenous nutrients were likely to reach waters around Magnetic Island. We speculate that higher abundance of Ce-oxidizing bacteria during strong flood events modulate local nearshore marine Ce anomalies. Based on these findings, we demonstrate that robust, time-resolved shale-normalized REE distributions in coral skeletons, not just elemental concentrations, provide very useful proxies for monitoring terrigenous sediment discharge related changes in inshore water quality and for tracing coastal biological activities, particularly at annual and multi-annual timescales.